Sequence
atgc intronic sequence ATGC exonic sequencegtatttgttattaaaatggttattgtcttgatgcttttaaaaaattgtatatgtgtgatcattattttttagctattctattcttctcccttgtgatatgtgtgcatacgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTAATTCTTCTTCCTTCAAATATTACTGTTTTTACCCTTGACTTCTCGGGGTCAGGCTTATCTGATGGA
Basic information
species | Glycine max |
transcript | GLYMA07G40050.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g10440.1 (Oryza sativa), 3'ss of exon 3
gtatttgttattaaaatggttattgtcttgatgcttttaaaaaattgtatatgtgtgatcattattttttagctattctattcttctcccttgtgatatgtgtgcatacgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTAATTCTTCTTCCTTCAAATATTACTGTTTTTACCCTTGACTTCTCGGGGTCAGGCTTATCTGATGGA
||||| || | || || || || | | ||| | | | | || || | || | | ||| | ||||| ||||||||| |||||||||| |||||||||||||| || || |||||| ||||||| ||||||||||| ||||| || || |||||||| |||| | ||||
------------------gttatgagctag-catttcctcttaactg-atgagattcatctcaagcaatcaccgatatcttttggaatctttaacaggcttttgctttgactcaatg---cagTGGATGCCGGGCAGATGCAAATGAAGCTGCTGTTATACTGCTTCCTGCAAATATCACTGTTTTTACACTTGATTTTTCCGGGTCAGGTCTATCAGGTGGA
upper sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g40730.1 (Oryza sativa), 3'ss of exon 3
gtatttgttattaaaatggttattgtcttgatgcttttaaaaaattgtatatgtgtgatcattattttttagctattctattcttctcccttgtgatatgtgtgcatacgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTAATTCTTCTTCCTTCAAATATTACTGTTTTTACCCTTGACTTCTCGGGGTCAGGCTTATCTGATGGA
| |||| |||| | | || | | | || | || || |||| | | | || || | | |||| | | | | | ||||| ||||||||| || || ||||| |||||||| ||||| || ||||| ||||||||||| || | ||||| |||||||| | |||||||| |||| | ||||
--------------gttagttacagtctctgagttattgaga-----tgaatcattaatt-ttgttttcttcttgtgcttatcgtattccttacaagctctttctcttaactcaatg---cagTGGATGCAGAGCGGATGCAAATGAAGCAGCTGTCATACTTCTCCCTTCAAATATCACCCTCTTTACACTTGACTTTGCAGGGTCAGGGCTATCAGGTGGA
upper sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G081642_T03 (Zea mays), 3'ss of exon 3
--------------------------gtatttgtt-----attaaaatggttattgtcttgat--gcttttaaaaaattgtatatgtgtgatcattattttttagctatt-ctattcttctcccttgtgatatgtgtgcatacg---tacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTAATTCTTCTTCCTTCAAATATTACTGTTTTTACCCTTGACTTCTCGGGGTCAGGCTTATCTGATGGA
| ||||||| ||| | | ||| || | | | ||||| || | ||| | || ||||| | | | | || || | | | | || | | | | |||||| ||||| | |||||||| |||||||| ||||| || ||||||||||||||||| |||||||| || |||||||| || |||||||| |||| | ||
gtatttaacttttatgctccatgtttgcatttgtttgacgattcatagggtgcttctttatctcaactttttaagacttggtt--gtatgatccagaagctcaaacaatcactggtatgttttggaatattaaacaggattttgctttgactcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAATATCACTGTTTTCACACTTGACTTTTCTGGGTCAGGTCTATCCGGCGGG
upper sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G081642_T04 (Zea mays), 3'ss of exon 3
gtatttgttattaaaatggttattgtcttgatgcttttaaaaaattgtatatgtgtgatcattattttttagctattctattcttctcccttgtgatatgtgtgcatacgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTAATTCTTCTTCCTTCAAATATTACTGTTTTTACCCTTGACTTCTCGGGGTCAGGCTTATCTGATGGA---------------------------
| |||||| ||||| | |||||||| |||||||| ||||| || ||||||||||||||||| |||||||| || |||||||| || |||||||| |||| | ||
-------------------------------------------------------------------------------------------------------------ttgactcaatgcagcggatgccgagcagatgcaaatgaagccgctgttatacttcttccttcaaatatcactgttttcacacttgacttttctgggtcagGTCTATCCGGCGGGGATTATGTCAGTTTGGGTTGGCATGAG
upper sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G092895_T01 (Zea mays), 3'ss of exon 3
gtatttgttattaaaatggttattgtcttgatgcttttaaaaaattgtatatgtgtgatcattattttttagctattctattct-tctcccttgtgatatgtgtgcatacgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTAATTCTTCTTCCTTCAAATATTACTGTTTTTACCCTTGACTTCTCGGGGTCAGGCTTATCTGATGGA
| || ||| | || | | ||| | | | ||| | || ||| | | | | | | || | || | |||||||||||| || |||||||| |||||||| ||||| || ||||||||||||||||| || ||||||| |||||||| |||| ||||| |||| ||||
------------------------gcctatgagctatcaagatgattcttatttccatttgctctttaccatcttcaatatccaatgtggttcatttaacaagttttttattaatttaatgcagTGGATGCAGAGCAGATGCAAATGAAGCCGCTGTCATACTTCTTCCTTCAAATATCACCCTTTTTACACTTGACTTTGCGGGATCAGGGCTATCAAGTGGA
upper sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 3
gtatttgttattaaaatggttattgtcttgatgcttttaaaaaattgtatatgtgtgatcattattttttagctattctattcttctcccttgtgatatgtgtgcatacgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTAATTCTTCTTCCTTCAAATATTACTGTTTTTACCCTTGACTTCTCGGGGTCAGGCTTATCTGATGGA
| | ||| ||| | | | | | | | | ||| | ||| | | | | || || || | | | | ||||||||||||||||||||| ||||| || | | | |||| || || || || || |||||||| |||||||||||||||||||||||||||||||| ||
----------------------gtacatagatacttgcacatctcttttaggaactaagaacttgtttatgactagttgaataaataagaacttaatccgtttgtttcggaatcttac--cagTGGATGTAGGGCAGATGCAAATGAGGCAGTTATGGTTCTCCTCCCATCTAACATAACTGTTTTCACCCTTGACTTCTCGGGGTCAGGCTTATCTGAGGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagctattctattcttctcccttgtgatatgtgtgcatacgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTAATTCTTCTTCCTTCAAATATTACTGTTTTTACCCTTGACTTCTCGGGGTCAGGCTTATCTGATGGA
tattctatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttgttattaaaatggttattgtcttgatgcttttaaaaaattgtatatgtgtgatcattattttttagctattctattcttctcccttgtgatatgtgtgcatacgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTAATTCTTCTTCCTTCAAATATTACTGTTTTTACCCTTGACTTCTCGGGGTCAGGCTTATCTGATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA