Contig : dd_Smed_v6_8075_0_1 S. mediterranea

Id  dd_Smed_v6_8075_0_1 Length  5191    Open in Genome Browser

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Planmine Rnai Result Displayer

Planmine Anatomy Displayer

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Planmine Timeseries Result Displayer

Planmine Regeneration Time Course Displayer

Homologue Displayer

Organism Field Displayer

Genes

GO Displayer

SequenceFeatures

3 Blast SequenceFeatures

Blast Target Species Blast Description evalue Contig Location Length Strand
NP_031763.2 Mus musculus collagen, type V, alpha 2 2.0E-53 1449-4034 2586 1
NP_000384.2 Homo sapiens collagen, type V, alpha 2 3.0E-48 2094-4142 2049 1
XP_001942763.2 Acyrthosiphon pisum fibril-forming collagen alpha chain-like 1.0E-105 1341-5012 3672 1

13 Domain SequenceFeatures

Domain Type InterPro Domain Description Score Contig Location Length Strand
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.4E-8 1107-1277 171 1
PF01410 PFAM IPR000885 Fibrillar collagen C-terminal domain 3.9E-41 4347-5009 663 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 4.4E-7 1251-1418 168 1
SM00210 SMART IPR001791 Thrombospondin N-terminal -like domains. 8.5E-5 249-788 540 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.5E-7 1404-1574 171 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 3.3E-7 3789-3962 174 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 6.0E-9 3978-4139 162 1
SSF49899 SSF IPR008985 Concanavalin A-like lectins/glucanases 7.62E-15 390-725 336 1
PTHR24023:SF351 PANTHER VIKING 3.0E-275 609-5012 4404 1
SM00038 SMART IPR000885 Fibrillar collagens C-terminal domain 1.1E-13 4284-5012 729 1
PTHR24023 PANTHER FAMILY NOT NAMED 3.0E-275 609-5012 4404 1
G3DSA:2.60.120.200 GENE3D IPR013320   7.4E-6 411-686 276 1
PS51461 PROFILE IPR000885 Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. 44.331 4287-5012 726 1

13 ORFs

Contig Location Length Strand Sequence
393-5015 4623 1
875-1222 348 -1
3031-3216 186 1
4001-4162 162 -1
1231-1383 153 -1
958-1101 144 1
1392-1535 144 -1
2113-2247 135 1
4911-5045 135 -1
1790-1912 123 -1
846-968 123 -1
1276-1389 114 1
3463-3576 114 1

1 Treefam SequenceFeatures

Gene Family Score Reading Frame Bit Score Coverage Contig Location Length Strand
TF316865 2.3E-135 3 451.2 0.449817 897-3231 2335 1
 

Other

0 Publications




To cite PlanMine, please refer to the following publication:

Brandl, H., Moon, H., Vila-Farré, M., Liu, S.-Y., Henry, I., & Rink, J. C.
PlanMine - a mineable resource of planarian biology and biodiversity.
Nucleic Acids Research, gkv1148. doi:10.1093/nar/gkv1148 (2015)