Contig : dd_Smed_v6_649_0_1 S. mediterranea

Id  dd_Smed_v6_649_0_1 Length  9405    Open in Genome Browser

J Browse Displayer

Planmine Rnai Result Displayer

Planmine Anatomy Displayer

Planmine Cell Type Displayer

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
XP_005750910.1 Pundamilia nyererei collagen alpha-1(I) chain-like 2.0E-34 8586-9248 663 1
XP_004572576.1 Maylandia zebra collagen, type I, alpha 1 3.0E-34 8586-9248 663 1
XP_007482462.1 Monodelphis domestica collagen alpha-1(I) chain-like 4.0E-33 8586-9248 663 1

30 Domain SequenceFeatures

Domain Type InterPro Domain Description Score Contig Location Length Strand
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 3.3E-8 8376-8549 174 1
PS51461 PROFILE IPR000885 Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. 46.287 8586-9248 663 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 6.4E-8 7575-7748 174 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 7.4E-7 8241-8405 165 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 1.4E-8 6258-6428 171 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 3.2E-7 7314-7475 162 1
PF01410 PFAM IPR000885 Fibrillar collagen C-terminal domain 7.2E-51 8643-9245 603 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.9E-6 7467-7634 168 1
SM00038 SMART IPR000885 Fibrillar collagens C-terminal domain 2.5E-34 8595-9248 654 1
PTHR24023 PANTHER FAMILY NOT NAMED 3.4E-242 5451-9248 3798 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.9E-7 5853-6023 171 1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 4.1E-7 7113-7286 174 1
PS51461 PROFILE IPR000885 Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. 42.351 284-961 678 -1
SM00038 SMART IPR000885 Fibrillar collagens C-terminal domain 9.6E-29 284-964 681 -1
PF01410 PFAM IPR000885 Fibrillar collagen C-terminal domain 7.4E-48 287-910 624 -1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.4E-5 4256-4363 108 -1
PS50184 PROFILE IPR001007 VWFC domain profile. 8.624 4493-4687 195 -1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 6.1E-8 3986-4153 168 -1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.4E-7 2522-2686 165 -1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 1.0E-7 2684-2857 174 -1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 3.5E-6 2987-3118 132 -1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 5.2E-9 3701-3874 174 -1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 3.9E-8 1517-1687 171 -1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 3.2E-8 1109-1273 165 -1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 2.9E-6 1253-1426 174 -1
PTHR24023 PANTHER FAMILY NOT NAMED 0.0 284-4771 4488 -1
PTHR24023:SF365 PANTHER PROTEIN COL-81 0.0 284-4771 4488 -1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 6.4E-8 2792-2965 174 -1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 3.2E-7 3854-4018 165 -1
PF01391 PFAM IPR008160 Collagen triple helix repeat (20 copies) 3.9E-7 1364-1534 171 -1

31 ORFs

Contig Location Length Strand Sequence
177-4769 4593 -1
5298-9251 3954 1
6490-7053 564 1
6310-6840 531 -1
2393-2860 468 1
1195-1491 297 1
3458-3727 270 -1
8374-8640 267 1
6806-7063 258 -1
7779-8030 252 -1
6065-6256 192 -1
8959-9123 165 1
7816-7977 162 1
1541-1699 159 -1
680-835 156 -1
337-489 153 1
1412-1564 153 1
777-926 150 1
9035-9181 147 -1
4986-5129 144 1
5608-5748 141 1
3872-4012 141 -1
955-1089 135 1
8698-8832 135 1
4163-4297 135 -1
3256-3372 117 1
3149-3265 117 -1
941-1057 117 -1
929-1042 114 1
5994-6104 111 -1

1 Treefam SequenceFeatures

Gene Family Score Reading Frame Bit Score Coverage Contig Location Length Strand
TF323987 5.6E-271 6 902.6 0.43561935 279-4377 4099 -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)