Sequence
atgc intronic sequence ATGC exonic sequence...atgctttattattgtaccatacaatatgcctgtgcttttgctggttctgtttaatttacttgtcatacttataatatggtatttcaataatacaatacagGTTTGAAGAAGTCATTGTTCAATGTCTTCCAAGATGGTTTATGCCATCCAAAGATGGCATTGGTAATTGATGATCGCTTGAAAGTGTGGGATGAGAAGGA
Basic information
species | Glycine max |
transcript | GLYMA07G31430.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G31430.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g44710.2 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------------------------------------------atgctttattattgtac-catacaatatgcctgtgcttttgctggttctgtttaatttacttgtcatacttataatatggtatttcaataatacaatacagGTTTGAAGAAGTCATTGTTCAATGTCTTCCAAGATGGTTTATGCCATCCAAAGATGGCATTGGTAATTGATGATCGCTTGAAAGTGTGGGATGAGAAGGA
|| | | | ||| ||||||| || | || || | ||| | | || ||| || | | | | || | | || ||| | ||||| || | ||||| ||||| ||||| | ||||| ||| | ||||| | || |||||||||||||||||||| ||||||||||| ||
gtaggtgttagcattactattactttcaaacaacacaactaccaaaggaatatagtgtcatttggtatattttgtacaccgcaatcaatgttttgtgttgtctaatttccttcatacaa-atttccatgtgcatgaacataatgtcttgga-attttccatcttttgacgttaatgctacaccactct--tatagGCTCTCGAAAGTCTCTGCTGAATGTATTCCATGATGGGTCTTGCCACCCAGAAATGGCCCTAGTGATTGATGATCGCTTGAAAGTTTGGGATGAGAAAGA
upper sequence: GLYMA07G31430.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------atgctttattattgtaccatacaata-tgcctgtgcttttgctggttctgtttaatttacttg--tcatacttataatatggtatttcaataatacaa--tacagGTTTGAAGAAGTCATTGTTCAATGTCTTCCAAGATGGTTTATGCCATCCAAAGATGGCATTGGTAATTGATGATCGCTTGAAAGTGTGGGATGAGAAGGA
|| | | | |||| | ||| | | || | | | || || || | | |||| || | | || || ||| | | | || |||||| || ||||| ||| | ||||||||||| ||||||| |||||||| |||||||| ||||||||||||||| ||||||| ||||||||||||||
gtatgtaattcatcttgtttttgaacaagtacaaaaagagcattagcctaatgtggcctaaatgttgtcatactcaaaagttgacaaactgtgaaaaatacaattcaaatttttagtttcattctactgaaatta-atgccaaatttcctatttatagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA
upper sequence: GLYMA07G31430.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 3
atgctttattattgtaccatacaatatgcctgtgcttttgctggttctgtttaatttacttgtcatacttataatatggtatttcaataatacaatacagGTTTGAAGAAGTCATTGTTCAATGTCTTCCAAGATGGTTTATGCCATCCAAAGATGGCATTGGTAATTGATGATCGCTTGAAAGTGTGGGATGAGAAGGA
| ||| | ||| | | | | ||| || | ||| || | || | |||| | || || ||| | || |||||||| || |||||| |||||||||| || | ||||| ||||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||
-----------gtatactttttggtat-cttatac-----ctgcttatatttcatca--tggtaaaacttct--tacaagcttgtaattaaccaccacagGTTTTAAAAAGTCACTGTTCAATGTGTTTCTCGATGGAACCTGCCATCCAAAGATGGCATTGGTAATTGATGATCGATTGAAAGTTTGGGATGAGAAGGA
upper sequence: GLYMA07G31430.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0370g00040.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------------------------------------atgctttattattgtaccatacaat--atgcctgtgctt-ttgctggttctgtt-taatttacttgtcatacttataatatggta-----tttcaataatacaat--acagGTTTGAAGAAGTCATTGTTCAATGTCTTCCAAGATGGTTTATGCCATCCAAAGATGGCATTGGTAATTGATGATCGCTTGAAAGTGTGGGATGAGAAGGA
| | | ||| | | | || | ||| || || || ||| | | ||| || | || ||||| || |||| || || | | | ||| | | |||||| ||||||||||||| |||||||| | |||||||| |||||||| || |||||||||||||| ||||||||||||||||| || ||
gtaagtttttaaaagaaatggttgatcttagggatgacttatgccatccacagcagaccaaagacaagctaattaattatatagcttctgatatgattttttttcacccattcttgtagttgttacttgttattctgtaaaccacgtacattatcctcaatatcctacttattttctttattaaatttgatagGCTCAAGAAAGTCACTGTTCAATGTCTTTCAAGATGGAATCTGCCATCCTAAGATGGCTTTAGTAATTGATGATCGTTTGAAAGTGTGGGATGAAAAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtttaatttacttgtcatacttataatatggtatttcaataatacaatacagGTTTGAAGAAGTCATTGTTCAATGTCTTCCAAGATGGTTTATGCCATCCAAAGATGGCATTGGTAATTGATGATCGCTTGAAAGTGTGGGATGAGAAGGA
gtttaat putative branch site (score: 4)
ttataatatggtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgctttattattgtaccatacaatatgcctgtgcttttgctggttctgtttaatttacttgtcatacttataatatggtatttcaataatacaatacagGTTTGAAGAAGTCATTGTTCAATGTCTTCCAAGATGGTTTATGCCATCCAAAGATGGCATTGGTAATTGATGATCGCTTGAAAGTGTGGGATGAGAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
-tgcttta
- - - - - - - - ccataca
- - - - - - - - - - - - tatgcct
- - - - - - - - - - - - - - - - - - tttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgtca