Sequence
atgc intronic sequence ATGC exonic sequence...cacctcaatgtcgcggtggtcacactgatttttagcttatccaagtttttcataatgttttttgtttgcctgtctaattgccaaatatacgtgtttgtagCTGAATGTTTCAAGGATAGAACTGATGTGCAATGCCTACATAGGTGGCAGAAAGTTTTAAATCCTGAACTTGTTAAAGGTCCATGGTCTAAAGAG
Basic information
species | Glycine max |
transcript | GLYMA17G26240.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G26240.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G531738_T01 (Zea mays), 3'ss of exon 1
cacctcaatgtcgcggtggtcacactgatttttagcttatccaagtttttcataatgttttttgtttgcctgtctaattgccaaatatacgtgtttgtagCTGAATGTTTCAAGGATAGAACTGATGTGCAATGCCTACATAGGTGGCAGAAAGTTTTAAATCCTGAACTTGTTAAAGGTCCATGGTCTAAAGAG
| | | | | ||||||| | | || | |||| ||| || || | | | | | | | |||||||||||| | ||| |||||||| ||||| | ||||| |||||||| ||||| || ||||| ||||||||||| || ||||| |||||
----------ctactattccatccttttccccttgcttatcaatgagaatctttatgtgaaactaatgcttgatgaactact-----tccttttccgcagctgaatgttttccagGTAGGACTGATGTTCAATGTTTGCATAGATGGCAGAAGGTTTTGAACCCTGAGCTTGTTAAAGGGCCTTGGTCGAAAGAA
upper sequence: GLYMA17G26240.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G11510.1 (Arabidopsis thaliana), 3'ss of exon 4
cacctcaatgtcgcggtggtcacactgattt-ttagcttatccaagtttttcataatgttttttgtttgcctgtctaattgccaaatatacgtgtttgtagCTGAATGTTTCAAGGATAGAACTGATGTGCAATGCCTACATAGGTGGCAGAAAGTTTTAAATCCTGAACTTGTTAAAGGTCCATGGTCTAAAGAG
|| | | | | | | | || ||| |||| |||| || |||| | || | | | | | | |||||||| ||||||||| |||||||||| || ||||| || |||||||| || || | |||||||||||||||||||| || ||| | || |||
---------gttgacattctttcctttctatattcatttactgaagtgaactgtaatcttccttgtctaaatgcatg-tcacatcttttcttaactctcagCTGAATACTTCAAGGATCGAACTGATGTCCAGTGCCTCCACAGGTGGCAAAAGGTCCTTAATCCTGAACTTGTTAAAGGGCCCTGGACGAAGGAG
upper sequence: GLYMA17G26240.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g03750.t01 (Vitis vinifera), 3'ss of exon 3
cacctcaatgtcgcggtggtcacactgatttttagcttatccaagtttttc-----ataatgttttttgtttgcctgtctaattgccaaatatacgtgtttgtagCTGAATGTTTCAAGGATAGAACTGATGTGCAATGCCTACATAGGTGGCAGAAAGTTTTAAATCCTGAACTTGTTAAAGGTCCATGGTCTAAAGAG
|||| | || | ||| | || |||||| |||| | ||| | | |||| ||| | |||| ||||||||||||||||||| | || ||||| || || | || |||||||||||||| |||||||||||||| | |||||||||||||||||||||
-----caatcataatggagttaatctgtgggagaaggaatgggagttttaacagagataagttatttcacaaacttccttaatatgtaaaccatctaatttgcagCTGAATGTTTCAAGGATCGGACCGATGTTCAGTGTTTGCACAGGTGGCAGAAAGTCTTAAATCCTGAACTCATCAAAGGTCCATGGTCTAAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttcataatgttttttgtttgcctgtctaattgccaaatatacgtgtttgtagCTGAATGTTTCAAGGATAGAACTGATGTGCAATGCCTACATAGGTGGCAGAAAGTTTTAAATCCTGAACTTGTTAAAGGTCCATGGTCTAAAGAG
gtctaat putative branch site (score: 3)
ataatgttttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacctcaatgtcgcggtggtcacactgatttttagcttatccaagtttttcataatgttttttgtttgcctgtctaattgccaaatatacgtgtttgtagCTGAATGTTTCAAGGATAGAACTGATGTGCAATGCCTACATAGGTGGCAGAAAGTTTTAAATCCTGAACTTGTTAAAGGTCCATGGTCTAAAGAG
cacctca
- - - - - - gcggtgg
- - - - - - - - - - cacactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccaaa