Sequence
atgc intronic sequence ATGC exonic sequence...gacacatgaatgattttgtattacaattctaactgttttatgttctagattgtgatcatgttacatcagttgacactaattttatttggtatgtgaacagTCTAGAGTAGTCCAATGCAATGAAGGGGAAAGATCATATCACATATTTTATCAGCTATGTGCTGGTGCACCTCCATCTCTCAGGG
Basic information
species | Glycine max |
transcript | GLYMA09G42180.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G139583_T02 (Zea mays), 3'ss of exon 8
gacacatgaatgattttgtattacaattctaactgttttatgttctagattgtgatcatgttacatcagttgacactaattttatttggt---atgtgaacagTCTAGAGTAGTCCAATGCAATGAAGGGGAAAGATCATATCACATATTTTATCAGCTATGTGCTGGTGCACCTCCATCTCTCAGGG
| || ||| || ||||| | | | || | |||| || ||| | | ||| || | || ||||| ||||| || ||||| | || ||| |||| || || |||||||||||||| ||||||||||||||| ||||||| || |
---------------gtaacttctaatctta--tgttt-gtccttagaaaaatggtagtgtttcactagtctaatatgccttttttcactttcattacggcagTCCAGAGTTGTGCAATGTGCAGTTGGTGAACGATCGTACCATATATTTTATCAGCTGTGTGCTGGTGCACCTGCATCTCTAAGAG
upper sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 8
gacacatgaatgattttgtattacaattctaactgttttatgttctagattgtgatcatgttacatcagttgaca--ctaat-tttatttggtatgtgaacagTCTAGAGTAGTCCAATGCAATGAAGGGGAAAGATCATATCACATATTTTATCAGCTATGTGCTGGTGCACCTCCATCTCTCAGGG
| | || || | | | | || | || | || |||| || ||| | | ||||| | ||| || ||||| ||||| || ||||| | || || ||||||| || |||||||||||||| || |||||||||||| | ||||| | |
---------gtaacttctaatcttatgtttgtcc--ttagaaaaatggactactatattgtttca-cagctattagtctaatatgccttttttaccacggcagTCCAGAGTTGTGCAATGTGCAGTTGGTGAGCGATCATACCATATATTTTATCAGCTGTGCGCTGGTGCACCTGCCTCTCTAAAAG
upper sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 10
gacacatgaatgattttgtattacaattctaactgttttatgt-tctagattgtgatcatgttacatcag--ttgacactaatt--ttatttggt-----atgtgaacagTCTAGAGTAGTCCAATGCAATGAAGGGGAAAGATCATATCACATATTTTATCAGCTATGTGCTGGTGCACCTCCATCTCTCAGGG
| || | | ||| || || || || | | | || | | |||| | ||| | |||||| | || || | || | || | ||||||||||||| |||||||| |||||||||||| |||||||| || |||||||| || |||||||| || | || | || || |
---------gtagcttctttggatgattttatttgcttgatttctttcctttttaaacatgattcattaacattgacattttttctttgtatgttgactcattttaacagTCTAGAGTGGTCCAATGTGCTGAAGGGGAAAGGTCATATCATATTTTTTATCAACTTTGTGCTGGGGCTTCACCTGCACTTAGAG
upper sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 8
gacacatgaatgattttgtattacaattctaactgttttatgttctagattgtgatcatgttacatcagttgacactaattttatttggtatgtgaacagTCTAGAGTAGTCCAATGCAATGAAGGGGAAAGATCATATCACATATTTTATCAGCTATGTGCTGGTGCACCTCCATCTCTCAGGG
| ||| | | || | | || || || | || ||| | |||| | | | | | | ||||| | | | | | ||||||||||||||| |||||||| ||||| || || |||||||| ||||||||||| || |||||||| || || ||| |||| || |
---------gtaattctttctt-tatctgtatctattgtttggtctg---tttgattttctcataatgggt--tgttaattgtgtctcttttatgaacagTCTAGAGTGGTCCAATGTGCAGAAGGAGAGAGGTCATATCATATATTTTATCAACTCTGTGCTGGAGCTCCACCAGCTCTTAGAG
upper sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 8
gacacatgaatgattttgtattacaattctaactgttttatgttctagattgtga-tcatgttacatcagttgacactaattt---tatt--tggtatgtgaacagTCTAGAGTAGTCCAATGCAATGAAGGGGAAAGATCATATCACATATTTTATCAGCTATGTGCTGGTGCACCTCCATCTCTCAGGG
| | || ||| ||||| | | | || | | || | || || | || ||| ||| || | || | || |||| || | | | ||||| ||||| || || ||||| ||||||||||||||| | |||||||| ||||||||||||| | |||| | | |
------ttagtggtttggtattcagagtattaccaaatgaggtcgttcatcgtatcttatcttatatctgtggttgcttagttatttattgttgttttatatgcagTCGAGAGTTGTACAGCAAGCAGAAGGCGAAAGATCATATCACGTTTTTTATCAATTATGTGCTGGTGCTGATGAATCTTTACGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagattgtgatcatgttacatcagttgacactaattttatttggtatgtgaacagTCTAGAGTAGTCCAATGCAATGAAGGGGAAAGATCATATCACATATTTTATCAGCTATGTGCTGGTGCACCTCCATCTCTCAGGG
cactaat putative branch site (score: 2)
taattttatttggtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gacacatgaatgattttgtattacaattctaactgttttatgttctagattgtgatcatgttacatcagttgacactaattttatttggtatgtgaacagTCTAGAGTAGTCCAATGCAATGAAGGGGAAAGATCATATCACATATTTTATCAGCTATGTGCTGGTGCACCTCCATCTCTCAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - catgaat
- - - - - - - - - - - - - - ctaactg
- - - - - - - - - - - - - - - - - - - - - - - -gattgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacact