Sequence
atgc intronic sequence ATGC exonic sequencegtaaaattcctaaaatttattagtctgaaatgattttccactaatcatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAATAAGCTTGTCTCTCAAATCAAGGGTACAACAAAGATTCCTGTTCTTGGTCATGCTG
Basic information
species | Glycine max |
transcript | GLYMA07G16510.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G16510.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
------gtaaaattcctaaaatttattagtctgaaatgatt--ttccactaa--tcatactttgcc--acagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAATAAGCTTGTCTCTCAAATCAAGGGTACAACAAAGATTCCTGTTCTTGGTCATGCTG
| ||||| | || | ||| | | || |||| | || | | ||||||||||| || || |||||||| | || ||||| |||||||||||||||||||||||||||| |||| ||||||||||||||||| |||||||
gtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacccgtaatacactgtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
upper sequence: GLYMA07G16510.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 12
--------gtaaaat--tcctaaaatttattagtct--gaaatgattttccactaatcatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAATAAGCTTGTCTCTCAAATCAAGGGTACAACAAAGATTCCTGTTCTTGGTCATGCTG
||||| | | || | || | | | ||| | | | | || | |||| || ||||||||||| ||||| |||||||| | || ||||| || |||||||| || || || ||||| | |||| |||||||||||||||||||||||||
gtgagtatgtaaagtgattctttgggtgataaatttaagaatttaatctaaaccagaagtactctgt-gcagCTTGATGATGTGATTGATCTTGTAATACCAAGAGGTAGCAATAAGCTCGTTTCCCAGATCAAAGCAGCAACCAAGATTCCTGTTCTTGGTCATGCTG
upper sequence: GLYMA07G16510.1 (Glycine max), 3'ss of exon 9
lower sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
----------------------------------------gtaaaattcctaaaatttattagtctga--aatgattttccactaatcatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAATAAGCTTGTCTCTCAAATCAAGGGTACAACAAAGATTCCTGTTCTTGGTCATGCTG
| ||| | | | | || | | || ||| | | ||| || |||| | | ||||||| |||| || || |||||||| | || |||||||| |||||||| || || ||||||||| |||| ||||| |||||||||||||||||||
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgat-tgtaccattatgcctaataagcctaaactcataatacact-ctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG
upper sequence: GLYMA07G16510.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G094309_T01 (Zea mays), 3'ss of exon 4
----------------gtaaaattcctaaaatttattagtctga--aatgattttccactaatcatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAATAAGCTTGTCTCTCAAATCAAGGGTACAACAAAGATTCCTGTTCTTGGTCATGCTG
| ||| | | | | || | | || ||| | | ||| || |||| | | ||||||| |||| || || |||||||| | || ||||| || |||||||| || || |||||||||| |||| ||||| |||||||||||||||||||
gtgagcgtaatatattatgaaaatgatgat-tgtaccattatgcctaataagcctaaactcataatacact-ctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGTAGCAATAAGCTGGTTTCACAAATCAAGGCATCAACTAAGATCCCTGTTCTTGGTCATGCTG
upper sequence: GLYMA07G16510.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0007g01060.t01 (Vitis vinifera), 3'ss of exon 12
---------------gtaaaattcctaaaatttattagtctgaaatgattttccactaatcatactt-tgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAATAAGCTTGTCTCTCAAATCAAGGGTACAACAAAGATTCCTGTTCTTGGTCATGCTG
| | | | | ||| | | | || || | ||| | || || |||| ||||||||||| || |||||||||||| |||| |||||||| || || || || ||||||||||||| | |||| || || |||||||||||||||||||
gtggggattgagattggatatgtttgatggtttttcataataggttggttattaacttgttttagttctgccccagCTTGATGATGTCATAGATCTTGTGATCCCTAGAGGCAGCAACAAACTCGTTTCTCAAATCAAGGATTCAACTAAAATCCCTGTTCTTGGTCATGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtctgaaatgattttccactaatcatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAATAAGCTTGTCTCTCAAATCAAGGGTACAACAAAGATTCCTGTTCTTGGTCATGCTG
aaatgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaattcctaaaatttattagtctgaaatgattttccactaatcatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAATAAGCTTGTCTCTCAAATCAAGGGTACAACAAAGATTCCTGTTCTTGGTCATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG