Sequence
atgc intronic sequence ATGC exonic sequence...taatcgcataatctgaactaagtttaccattatcatgttcaatactatcccatgtttcactagttgagcaataatttaaagaaaatacattcttaaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCTCACAATCTTGATTTCCGTGGTAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
Basic information
species | Glycine max |
transcript | GLYMA04G24350.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G24350.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
taatcgcataatctgaactaagtttaccattatcatgttcaatactatcccatgtttcactagttgagcaataatttaaagaaaatacattcttaaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCTCACAATCTTGATTTCCGTGGTAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | | | || | || | || | |||| | || |||| | | | || ||| | || ||||||||| || || ||||||| ||| ||||| || ||||||||||| || ||||||||||| ||||| | ||||| ||||||||| | ||| | | || |||
---gtacgtgacataaatt---ttcattctttgtaccttcagatatttcttcagttttttttttcg-----tatgttatgacactaccacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
upper sequence: GLYMA04G24350.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G115564_T01 (Zea mays), 3'ss of exon 8
taatcgcataatctgaactaa-gtttaccattatcatgttcaatactatcccatgtttcactagttgagcaataatttaaagaaaatacattctt-------aaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCTCACAATCTTGATTTCCGTGGTAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | || || | |||| | | ||||| | || | | | || | || | | ||| | |||||||| || || ||||||| ||| ||||| || |||||||| ||||||||| | ||||||||||| | ||||| ||||||||||||||||||| ||| |||
---gtatgcagcataaataaatactgttcattcttgc-tgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
upper sequence: GLYMA04G24350.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G370326_T01 (Zea mays), 3'ss of exon 7
taatcgcataatctgaactaa-gtttaccattatcatgttcaatactatcccatgtttcactagttgagcaataatttaaagaaaatacattctt-------aaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCTCACAATCTTGATTTCCGTGGTAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | || | || |||| | | ||||||| || | ||| || | || | | ||| | |||||||| || || ||||||| ||| ||||| || |||||||| ||||||||| | |||||| |||| | ||||| ||||||||||||||||||| ||| |||
---gtatgcagcataaataattattgttcattcttgc-tgagatactatggtgcagtttatatgttattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCTGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
upper sequence: GLYMA04G24350.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G440258_T01 (Zea mays), 3'ss of exon 5
taatcgcataatctgaactaagtttaccatta--tcatgttca-atactatcccatgtttcactagttgagcaataatttaaagaaaatacattctt-------aaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCTCACAATCTTGATTTCCGTGGTAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | || | |||| || || || | | |||| | || | | | || || || | | ||| | |||||||| || | ||||||| ||| ||||| || |||||||| ||||||||| | ||||||||||| | ||||| ||||||||||||||||||| ||| |||
---gtatgcagcataaataa---ttactgttcattcttgctgagataccgtggtgcagtttatatgctattacattgttggaattatacttgttccttttctgtaaacagGTTGCTCATAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
upper sequence: GLYMA04G24350.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G528717_T01 (Zea mays), 3'ss of exon 5
taatcgcataatctgaactaagtttaccatta--tcatgttca-atactatcccatgtttcactagttgagcaataatttaaagaaaatacattctt-------aaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCTCACAATCTTGATTTCCGTGGTAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | || | |||| || || || | | ||||| | || | | | || | || | | ||| | |||||||| || || ||||||| ||| ||||| | |||||||| ||||||||| | ||||||||||| | ||||| ||||||||||||||||||| ||| |||
---gtatgcagcataaataa---ttactgttcattcttgctgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGAATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
upper sequence: GLYMA04G24350.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G133353_T01 (Zea mays), 3'ss of exon 3
taatcgcataatctgaactaagtttaccatta--tcatgttca-atactatcccatgtttcactagttgagcaataatttaaagaaaa----tacattct---taaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCTCACAATCTTGATTTCCGTGGTAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | || | |||| ||| || || | | ||||| | || | | | || | || | | | |||| | ||||||||| || || ||||||| ||| ||||| | |||||||| ||||||||| | |||||| |||| | ||||| ||||||||||||||||||| ||| |||
---gtatgcagcataaataa---ttactattcattcttgctgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttcattttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGAATTTTATTACCCTCACAATTTAGATTTCTGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
upper sequence: GLYMA04G24350.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G319000_T01 (Zea mays), 3'ss of exon 4
taatcgcataatctgaactaagtttaccatta--tcatgttca-atactatcccatgtttcactagttgagcaataatttaaagaaaatacattctt-------aaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCTCACAATCTTGATTTCCGTGGTAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | || | |||| || || || | | ||||| | || | | | || | || | | ||| | |||||||| || || ||||||| ||| ||||| | |||||||| ||||||||| | |||||||||| | ||||| ||||||||||||||||||| ||| |||
---gtatgcagcataaataa---ttactgttcattcttgctgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGAATTTTATTACCCTCACAATTTATATTTCCGTGGGTGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
upper sequence: GLYMA04G24350.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G467606_T01 (Zea mays), 3'ss of exon 5
taatcgcataatctgaactaagtttaccatta--tcatgttca-atactatcccatgtttcactagttgagcaataatttaaagaaaatacattctt-------aaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCTCACAATCTTGATTTCCGTGGTAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | || | |||| || || || | | ||||| | || | | | || | || | | ||| | |||||||| || || ||| ||| ||| ||||| | |||||||| ||||||||| | ||||||||||| | ||||| | ||||||||||||||||| ||| |||
---gtatgcagcataaataa---ttactgttcattcttgctgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAGTGAGAGAGGAGGATAGATTTTATTACCCTCACAATTTAGATTTCCGTGGGTGTGCATACCTTATGCATCCTCATTTGAGTCACCTAG
upper sequence: GLYMA04G24350.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G475968_T01 (Zea mays), 3'ss of exon 7
taatcgcataatctgaactaagtttaccatta--tcatgttca-atactatcccatgtttcactagttgagcaataatttaaagaaaatacattctt-------aaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCTCACAATCTTGATTTCCGTGGTAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | || | |||| || || || | | ||||| | || | | | || | || | | ||| | |||||||| || || ||||||| ||| ||||| | |||||||| ||||||||| | ||||| |||| | ||||| ||||||||||||||||||| ||| |||
---gtatgcagcataaataa---ttactgttcattcttgctgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGAATTTTATTACCCTCACAATTTAGATTTTTGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
upper sequence: GLYMA04G24350.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0037g00630.t01 (Vitis vinifera), 3'ss of exon 8
taatcgcataatctgaactaagtttaccattatcatgttcaatactatcccatg-tttcactagtt---gagcaataatttaaagaaaatacattcttaaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCTCACAATCTTGATTTCCGTGGTAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | |||| | | || ||| |||| | | || | || | || ||| | | ||| | || |||| || |||||||||| ||||||||||||||||| |||||||||||||||||||||||||||||||| || || | || || || |||||||| |||||||||||| |
---tttcctaatgcagatttgattatgtattgccatgactggaagtctcgaagaactttgttcatttgtaagcttcagtgctaagcagattcatt-ttgaacagGTGGCTCGAAAAATGAAAGATGAAGAAGGCTTTTATTATCCTCACAATCTTGATTTTCGAGGCCGTGCGTACCCAATGCATCCACATTTGAATCATCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcccatgtttcactagttgagcaataatttaaagaaaatacattcttaaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCTCACAATCTTGATTTCCGTGGTAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
cattctt CT-rich tract
aataatttaaagaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatcgcataatctgaactaagtttaccattatcatgttcaatactatcccatgtttcactagttgagcaataatttaaagaaaatacattcttaaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCTCACAATCTTGATTTCCGTGGTAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - -tctgaac
- - - - - - - - - - - - - - - - -catgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa