Transcript : dd_Smed_v6_840_0_1 S. mediterranea

Length  4410     Open in Genome Browser Source  Transcriptome assembly (Trinity v2.2.0)
Published Transcripts 
EST: AY068366.1, clone H.1.12e unknown mRNA sequence
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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_034060.2 Mus musculus collagen, type III, alpha 1 4.0E-32 3619-4239 621 1
NP_000079.2 Homo sapiens collagen, type I, alpha 1 2.0E-14 571-1722 1152 1
XP_006025957.1 Alligator sinensis collagen, type I, alpha 2 1.0E-37 3622-4239 618 1

11 Domain Sequence Features

Domain Type InterPro Domain Description Score Contig Location Length Strand
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 6.0E-9 475-642 168 1
PTHR24023 PANTHER FAMILY NOT NAMED 1.1E-246 475-4239 3765 1
PS51461 PROFILE IPR000885 Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. 46.454 3568-4239 672 1
SM00038 SMART IPR000885 Fibrillar collagens C-terminal domain 3.1E-28 3586-4239 654 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 4.4E-6 937-1098 162 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 7.1E-8 2089-2256 168 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 7.1E-8 781-948 168 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 7.5E-7 1477-1650 174 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.0E-7 631-801 171 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 5.2E-8 3361-3531 171 1
PF01410 PFAM IPR000885 Fibrillar collagen C-terminal domain 4.2E-53 3625-4236 612 1

Genomics

Predicted Gene Displayer

J Browse Displayer

Homologue Displayer

22 ORFs

Contig Location Length Strand Sequence
361-4242 3882 1
2742-3137 396 -1
2336-2713 378 1
1572-1850 279 -1
1869-2084 216 -1
3701-3910 210 1
729-935 207 -1
40-216 177 -1
2789-2959 171 1
1889-2050 162 1
176-328 153 -1
137-286 150 1
3700-3849 150 -1
899-1039 141 1
1520-1660 141 1
4271-4408 138 -1
4135-4263 129 -1
1394-1516 123 1
4101-4217 117 -1
575-688 114 1
3203-3307 105 1
2975-3076 102 1

1 Treefam Sequence Features

Gene Family Score Reading Frame Bit Score Coverage Contig Location Length Strand
TF316865 1.2E-106 1 355.9 0.40498868 474-2259 1786 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)