Transcript : dd_Smed_v6_702_0_1 S. mediterranea

Length  4112     Open in Genome Browser Source  Transcriptome assembly (Trinity v2.2.0)
Published Transcripts 
EST: AY068300.1, clone H.68.5d(T3) unknown mRNA sequence
 Feedback

Organism Field Displayer

Association Displayer

Sequence Features

GO Displayer

3 Blast Sequence Features

Blast Target Species Blast Description evalue Contig Location Length Strand
NP_776945.1 Bos taurus collagen, type I, alpha 2 2.0E-31 3297-3995 699 1
XP_005909757.1 Bos mutus collagen, type I, alpha 2 2.0E-31 3297-3995 699 1
XP_005985745.1 Pantholops hodgsonii collagen, type I, alpha 2 2.0E-31 3297-3995 699 1

11 Domain Sequence Features

Domain Type InterPro Domain Description Score Contig Location Length Strand
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 1.1E-5 3114-3284 171 1
SM00038 SMART IPR000885 Fibrillar collagens C-terminal domain 2.8E-34 3339-3995 657 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 4.8E-6 2313-2483 171 1
PS51461 PROFILE IPR000885 Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. 47.456 3324-3995 672 1
PTHR24023:SF351 PANTHER VIKING 3.6E-232 210-3995 3786 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 1.5E-7 240-410 171 1
PF01410 PFAM IPR000885 Fibrillar collagen C-terminal domain 1.4E-53 3378-3992 615 1
PTHR24023 PANTHER FAMILY NOT NAMED 3.6E-232 210-3995 3786 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.2E-7 2052-2222 171 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.3E-5 2952-3110 159 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 7.1E-7 1860-2018 159 1

Genomics

Predicted Gene Displayer

J Browse Displayer

Homologue Displayer

14 ORFs

Contig Location Length Strand Sequence
144-3998 3855 1
1966-2472 507 1
1120-1425 306 1
3138-3443 306 -1
3212-3379 168 -1
3453-3605 153 -1
2806-2937 132 1
3103-3234 132 1
1095-1226 132 -1
1522-1650 129 1
3496-3612 117 1
364-477 114 1
652-765 114 1
2681-2788 108 -1

2 Treefam Sequence Features

Gene Family Score Reading Frame Bit Score Coverage Contig Location Length Strand
TF316865 1.5E-99 3 332.3 0.4686284 240-2166 1927 1
TF323987 2.7E-118 3 395.9 0.47519454 2040-3993 1954 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)