Transcript : dd_Smed_v6_2337_0_1 S. mediterranea

Length  5944     Open in Genome Browser Source  Transcriptome assembly (Trinity v2.2.0)
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Organism Field Displayer

Association Displayer

Sequence Features

GO Displayer

3 Blast Sequence Features

Blast Target Species Blast Description evalue Contig Location Length Strand
NP_723044.1 Drosophila melanogaster Collagen type IV 3.0E-67 519-3878 3360 1
NP_031763.2 Mus musculus collagen, type V, alpha 2 8.0E-33 1092-3560 2469 1
NP_000384.2 Homo sapiens collagen, type V, alpha 2 4.0E-32 540-3113 2574 1

29 Domain Sequence Features

Domain Type InterPro Domain Description Score Contig Location Length Strand
SSF118359 SSF IPR026939 Expressed protein At2g23090/F21P24.15 8.24E-5 5146-5241 96 1
PS51403 PROFILE IPR001442 Collagen IV carboxyl-terminal non-collagenous (NC1) domain profile. 48.503 4848-5525 678 1
PF01413 PFAM IPR001442 C-terminal tandem repeated domain in type 4 procollagen 1.8E-23 4854-5171 318 1
PF01413 PFAM IPR001442 C-terminal tandem repeated domain in type 4 procollagen 1.9E-28 5184-5519 336 1
PTHR24023 PANTHER FAMILY NOT NAMED 9.0E-250 330-5522 5193 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 6.9E-7 2850-3014 165 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 9.7E-9 396-569 174 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 1.8E-7 3474-3626 153 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 7.4E-6 1353-1514 162 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 1.9E-7 3174-3335 162 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 3.9E-7 2556-2729 174 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.0E-7 1146-1310 165 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.7E-6 3756-3911 156 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 6.5E-7 549-707 159 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 4.3E-6 3573-3737 165 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 1.5E-7 3894-4058 165 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 8.0E-7 2430-2597 168 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 1.2E-7 459-614 156 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.3E-6 2202-2363 162 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 1.2E-8 744-899 156 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 6.7E-8 2094-2246 153 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 1.2E-8 3033-3191 159 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 3.0E-9 1011-1181 171 1
SSF56436 SSF IPR016187 C-type lectin-like 3.77E-26 5181-5522 342 1
G3DSA:2.170.240.10 GENE3D IPR001442 Noncollagenous (NC1) domain of collagen IV 2.2E-70 4845-5522 678 1
SM00111 SMART IPR001442 C-terminal tandem repeated domain in type 4 procollagens 2.5E-27 5178-5522 345 1
SM00111 SMART IPR001442 C-terminal tandem repeated domain in type 4 procollagens 6.7E-27 4851-5174 324 1
PTHR24023:SF354 PANTHER SUBFAMILY NOT NAMED 9.0E-250 330-5522 5193 1
SSF56436 SSF IPR016187 C-type lectin-like 5.42E-27 4854-5177 324 1

Genomics

Predicted Gene Displayer

J Browse Displayer

Homologue Displayer

19 ORFs

Contig Location Length Strand Sequence
213-5528 5316 1
2300-2641 342 -1
125-409 285 -1
4529-4780 252 -1
4268-4483 216 -1
1108-1320 213 1
2830-3033 204 1
3937-4140 204 1
5711-5914 204 1
3633-3782 150 -1
2092-2232 141 1
3544-3666 123 1
655-774 120 1
4636-4755 120 1
5268-5387 120 -1
5747-5863 117 -1
4321-4434 114 1
1458-1565 108 -1
4874-4978 105 -1

1 Treefam Sequence Features

Gene Family Score Reading Frame Bit Score Coverage Contig Location Length Strand
TF316865 2.7E-212 3 706.5 0.5775572 2091-5523 3433 1

Expression Information

Planmine Rnai Result Displayer

Planmine Anatomy Displayer

Planmine Cell Type Displayer

Planmine Single Cell Displayer

Planmine Timeseries Result Displayer

Planmine Regeneration Time Course Displayer

Planmine Additional Displayer




To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)