Transcript : dd_Smed_v6_1070_0_1 S. mediterranea

Length  4228     Open in Genome Browser Source  Transcriptome assembly (Trinity v2.2.0)
Published Transcripts 
EST: AY067032.1, clone HB.8.10d unknown mRNA sequence
AY967621.1, clone NBE.4.11G 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
XP_003745135.1 Metaseiulus occidentalis collagen alpha-1(II) chain-like 4.0E-35 3031-4050 1020 1
XP_004923583.1 Bombyx mori collagen alpha-1(II) chain-like 4.0E-34 3379-4050 672 1
XP_004534844.1 Ceratitis capitata collagen alpha-1(II) chain-like 5.0E-31 3379-4050 672 1

11 Domain Sequence Features

Domain Type InterPro Domain Description Score Contig Location Length Strand
PS51461 PROFILE IPR000885 Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. 40.252 3409-4041 633 1
SM00038 SMART IPR000885 Fibrillar collagens C-terminal domain 1.1E-17 3418-4047 630 1
PTHR24023:SF362 PANTHER COLLAGEN ALPHA-1(XXVII) CHAIN 1.1E-244 205-4047 3843 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.8E-8 3196-3366 171 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 7.2E-8 313-483 171 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 9.0E-7 2125-2286 162 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 4.4E-8 1510-1680 171 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.5E-8 3070-3231 162 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.3E-7 1924-2097 174 1
PF01410 PFAM IPR000885 Fibrillar collagen C-terminal domain 1.1E-44 3457-4044 588 1
PTHR24023 PANTHER FAMILY NOT NAMED 1.1E-244 205-4047 3843 1

Genomics

Predicted Gene Displayer

J Browse Displayer

Homologue Displayer

14 ORFs

Contig Location Length Strand Sequence
175-4050 3876 1
831-1244 414 -1
2501-2905 405 -1
2157-2498 342 -1
275-580 306 -1
572-802 231 1
2186-2401 216 1
1301-1489 189 1
1760-1891 132 1
3720-3845 126 -1
50-169 120 -1
2546-2662 117 1
1148-1261 114 1
3833-3946 114 -1

2 Treefam Sequence Features

Gene Family Score Reading Frame Bit Score Coverage Contig Location Length Strand
TF316865 1.0E-102 1 342.9 0.4720908 1053-3048 1996 1
TF323987 8.9E-123 1 410.7 0.43803218 2127-3978 1852 1

Expression Information

Planmine Rnai Result Displayer

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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)