Sequence
atgc intronic sequence ATGC exonic sequence...atattttttgctttacatctaacctaatgtctctttccacatctcttgattaaaacattttacttactatatatttgttatcctgtgtgatgattaacagGATGAAAAGTATTGGCCACTGATGCCTGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCCGGTCCTCGATATAGTAGTTTAATTCATGGTCAAAATC
Basic information
species | Glycine max |
transcript | GLYMA15G19820.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G19820.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G348602_T01 (Zea mays), 3'ss of exon 1
atattttttgctttacatctaacctaatgtctctttccacatctcttgattaaaacattttacttactatatatttgttatcctgtgtgatgattaacagGATGAAAAGTATTGGCCACTGATGCCTGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCCGGTCCTCGATATAGTAGTTTAATTCATGGTCAAAATC
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---------------------------------------------------------gtgagcttatttaactggcattgtgatgttttctgg---acagGATGAGAAGTACTGGCCATTGATGCCAGCATTACCGTCATATGGGTATGGGCGGGAGCGCAAAGGACCACGATTTGGGAGCCTCATTCATGGACAGAATT
upper sequence: GLYMA15G19820.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G047414_T01 (Zea mays), 3'ss of exon 1
atattttttgctttacatctaacctaatgtctctttccacatctcttgattaaaacattttacttactatatatttgttatcctgtgtgatgatt----aacagGATGAAAAGTATTGGCCACTGATGCCTGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCCGGTCCTCGATATAGTAGTTTAATTCATGGTCAAAATC
| |||| | | ||| | || | ||| | | | | | ||||| | ||||||| || ||||||||| ||||| |||||| ||||||| ||||| || |||||||||||||| |||||| || || |||| | | || | |||||||| || |||
-cagagtttggtagatgccta---tggtgcttatttgggggcacaaatgcccacatttcagattgtgagcttatttaactggcattgtgatgttttctggacagGATGAGAAGTACTGGCCATTGATGCCAGCATTACCGTCATATGGGTATGGGCGGGAGCGCAAAGGACCACGATTTGGGAGCCTCATTCATGGACAGAATT
upper sequence: GLYMA15G19820.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------atattttttgc-tttacatctaacctaatgtctctttccacatctcttgattaaaacattttacttactatatatttgttatcctgtgtgatgattaacagGATGAAAAGTATTGGCCACTGATGCCTGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCCGGTCCTCGATATAGTAGTTTAATTCATGGTCAAAATC
| | | || ||| || || | | || | | | ||| | | || | ||| | ||| | || ||||||||||||||||| | || | ||| | || ||||||||||| |||||||| ||||||| || ||||| ||| | ||||| |||||||| || ||||
gttttgtttcctctgatttgaaattgtgatctatgtgtttgggatctgtttagggttttgatgcagagtttgttatttggttcactattgaattaagattgggttttgatgttgaaacgtttttagGATGAAAAGTATTGGTCTTTGCTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATC
upper sequence: GLYMA15G19820.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0016g00720.t01 (Vitis vinifera), 3'ss of exon 1
-atattttttgctttacatctaacctaatgtctctttccacatctcttgattaaaacattttacttactatatatttgttatcctgtgtgatgattaacagGATGAAAAGTATTGGCCACTGATGCCTGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCCGGTCCTCGATATAGTAGTTTAATTCATGGTCAAAATC
||||| | || || | | | || || | || | | ||| |||| | | | | | || | ||||| |||||||||||| ||||||||||||||||||||| | |||||||||||||||||||| || ||||||| || |||||||| | ||||| ||||||||||||||||
gatattcaataaactat-catattatgactagtgttagcatttatcgtataagcgaagtttggcttattttggttctttcttcttatgtgacatttaacagGATGAGAAGTATTGGCCACTGATGCCTCCCTTGCCTTCATATGGGTATGGGAGAGAGCATCGTGGAGCTCGATATGGGAGTTTGATTCATGGTCAAAATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattaaaacattttacttactatatatttgttatcctgtgtgatgattaacagGATGAAAAGTATTGGCCACTGATGCCTGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCCGGTCCTCGATATAGTAGTTTAATTCATGGTCAAAATC
tacttac putative branch site (score: 1)
taaaacattttactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atattttttgctttacatctaacctaatgtctctttccacatctcttgattaaaacattttacttactatatatttgttatcctgtgtgatgattaacagGATGAAAAGTATTGGCCACTGATGCCTGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCCGGTCCTCGATATAGTAGTTTAATTCATGGTCAAAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - tgcttta
- - - - - - - - - - - - - - - - - - ccacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgtgt