Sequence
atgc intronic sequence ATGC exonic sequencegtaaaattcctaaaatttatttgtctgaaatgattttcaactaattatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAACAAACTTGTTTCTCAAATCAAGGATTCCACAAAGATTCCTGTTCTTGGTCATGCTG
Basic information
species | Glycine max |
transcript | GLYMA18G40770.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G40770.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
-------------gtaaaattcctaaaatttatttgtctgaaatgattttcaactaattatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAACAAACTTGTTTCTCAAATCAAGGATTCCACAAAGATTCCTGTTCTTGGTCATGCTG
| ||| ||| | | ||| | ||| | |||| || ||||||||||| || || |||||||| | || ||||| ||||| || ||||| ||||||||||||| || || ||||||||||||||||| |||||||
gtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacccgtaatacactgt-gcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
upper sequence: GLYMA18G40770.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 12
--------gtaaa---attcctaaaatt-tatttgtctgaaatgattttcaactaattatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAACAAACTTGTTTCTCAAATCAAGGATTCCACAAAGATTCCTGTTCTTGGTCATGCTG
||||| |||| | | || | | ||| | | | | ||| | |||| || ||||||||||| ||||| |||||||| | || ||||| || || || || ||||| || ||||| | | || |||||||||||||||||||||||||
gtgagtatgtaaagtgattctttgggtgataaatttaagaatttaatctaaaccagaagtactctgt-gcagCTTGATGATGTGATTGATCTTGTAATACCAAGAGGTAGCAATAAGCTCGTTTCCCAGATCAAAGCAGCAACCAAGATTCCTGTTCTTGGTCATGCTG
upper sequence: GLYMA18G40770.1 (Glycine max), 3'ss of exon 13
lower sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
----------------------------------------gtaaaattcctaaa-atttatttgtctgaaatgattttcaactaattatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAACAAACTTGTTTCTCAAATCAAGGATTCCACAAAGATTCCTGTTCTTGGTCATGCTG
| ||| | | | | || | ||| | | |||| || |||| | | ||||||| |||| || || |||||||| | || |||||||| || || || ||||| ||||||||| || || ||||| |||||||||||||||||||
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacact-ctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
upper sequence: GLYMA18G40770.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G094309_T01 (Zea mays), 3'ss of exon 4
----------------gtaaaattcctaaa-atttatttgtctgaaatgattttcaactaattatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAACAAACTTGTTTCTCAAATCAAGGATTCCACAAAGATTCCTGTTCTTGGTCATGCTG
| ||| | | | | || | ||| | | |||| || |||| | | ||||||| |||| || || |||||||| | || ||||| || || || || ||||| |||||||||| || || ||||| |||||||||||||||||||
gtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacact-ctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGTAGCAATAAGCTGGTTTCACAAATCAAGGCATCAACTAAGATCCCTGTTCTTGGTCATGCTG
upper sequence: GLYMA18G40770.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv08s0007g01060.t01 (Vitis vinifera), 3'ss of exon 12
--------------gtaaaattcctaaaatttatttgtc-tgaaatgattttcaactaattatactt-tgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAACAAACTTGTTTCTCAAATCAAGGATTCCACAAAGATTCCTGTTCTTGGTCATGCTG
| || | | || || | | || || | |||| || || || |||| ||||||||||| || |||||||||||| |||| |||||||| |||||||| |||||||||||||||||||| || || || |||||||||||||||||||
gtggggattgagattggatatgtttgatggtttttcataataggttggttattaacttgttttagttctgccccagCTTGATGATGTCATAGATCTTGTGATCCCTAGAGGCAGCAACAAACTCGTTTCTCAAATCAAGGATTCAACTAAAATCCCTGTTCTTGGTCATGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtctgaaatgattttcaactaattatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAACAAACTTGTTTCTCAAATCAAGGATTCCACAAAGATTCCTGTTCTTGGTCATGCTG
aaatgattttcaacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaattcctaaaatttatttgtctgaaatgattttcaactaattatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAACAAACTTGTTTCTCAAATCAAGGATTCCACAAAGATTCCTGTTCTTGGTCATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG