Sequence
atgc intronic sequence ATGC exonic sequence...caatttgtgttgatattttaatttgactaaattctttggacagatgttctgtttttgttttgcttattccaatctgtttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCGGTGGAAGGACCAATCCCTCCGTCAAGAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA
Basic information
species | Glycine max |
transcript | GLYMA07G36340.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G36340.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g04020.1 (Oryza sativa), 3'ss of exon 6
-caatttgtgttgatattttaatttgactaaattctttggacagatgttctgtttttgttttgcttattccaatctgtttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCGGTGGAAGGACCAATCCCTCCGTCAAGAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA
|| | | | | || | | | | | | ||| | | | || | | ||| || | |||| | | |||||||||||| ||||| || ||||| ||||| || ||||| |||| | ||| |||| || |||||||||||||| || || ||||| |||||||||| ||
gtaagtcacataagcttgatgatctatcgagcctgaaagttaaaatgaacagacagcaatctgatc-tgagaatttg-----caaaatttgattgtcatagGTATGTTTCATGTGTGGTTGGTTGCCCTGTTGAAGGCACAATTCATCCATCAAAGGTAGCATATGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAG
upper sequence: GLYMA07G36340.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g04210.1 (Oryza sativa), 3'ss of exon 6
-caatttgtgttgatattttaatttgactaaattctttggacagatgttctgtttttgttttgcttattccaatctgtttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCGGTGGAAGGACCAATCCCTCCGTCAAGAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA
|| | | | | || | | | | | | | | | | | || | | ||| || | |||| | |||||||||||| ||||| || ||||| ||||| || ||||| |||| | ||| |||| || ||||| |||||||| || || ||||| |||||||||| ||
gtaagtcacataagcttgatgatctatcgagcctgaaagttaaaaagaacagacagcaatctgatc-tgagaatttgcata-----atttgatcgtcatagGTATGTTTCATGTGTGGTTGGTTGCCCTGTTGAAGGCACAATTCATCCATCAAAGGTAGCATACGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAG
upper sequence: GLYMA07G36340.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 5
-caatttgtgttgatattttaatttgactaaattctttggacag--atgttctgtttttgttttgcttattccaatctgtttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCGGTGGAAGGACCAATCCCTCCGTCAAGAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA
| | ||| | | ||||| | | | || | || || | ||||| ||||| ||| | | | || | ||| | ||| |||||||||| ||||| || ||||| || |||||||||||| | || |||| |||| ||| |||||||| || |||||||| |||||||||||||||||||||
ttactccatgtattaactcatgtttgaatgcttccaatgaaaagcaataatatgtttctgtttctgttactgaattgaagttg---gcattacattttgatagGTATGTGTCATGTGTCGTTGGGTGTCCGGTGGAAGGAGCTATTTCTCCCTCAAAAGTTGCATATGTGGCCAAAGAACTTTATGATATGGGTTGCTTTGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctgtttttgttttgcttattccaatctgtttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCGGTGGAAGGACCAATCCCTCCGTCAAGAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA
tgtatttaaatttcat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatttgtgttgatattttaatttgactaaattctttggacagatgttctgtttttgttttgcttattccaatctgtttctctgtatttaaatttcatagGTATGTATCATGCGTTGTTGGATGCCCGGTGGAAGGACCAATCCCTCCGTCAAGAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - -tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctgta