Sequence
atgc intronic sequence ATGC exonic sequence...aatgctaattcttgttctcttccttttgtttagtattactagtggcaaatgggaaagtttgactgtgacaataggaacctgccttgtttcatttccacagCTTACACTTATTTTCTTATTATTGTCAGGAATGGTAGCAGCCCTTACCAATGAGAGTGCTACCAGCAAATCTGTATACTTTGCACACTGCACATCAGAGA
Basic information
| species | Glycine max |
| transcript | GLYMA02G33340.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G33340.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 3
aatgctaattcttgttctcttccttttgtttagtattactagtggcaaatgggaaagtttgactgtgacaataggaacctgccttgtttcatttccacagCTTACACTTATTT----TCTTATTATTGT-CAGGAATGGTAGCAGCCCTTACCAATGAGAGTGCTACCAGCAAATCTGTATACTTTGCACACTGCACATCAGAGA----------------------------
| | | |||| || || | | | | ||| || | | || || ||| | || | || | | | || |||| | |||| ||||| ||||| || || ||||||||||| ||||||||||| || |||||||| | |||||||| || |
---------------------------gctatgctttac--gtcgcgtttt----aatcttgtcgtggtcatctgcctttttttttcttggtttatgcttctgttaattttctgaaattttgttatcctgcagGTATGGTGGCAGCTCTAACAAATGAGAGTGCAACCAGCAAATCCGTTTACTTTGCTCTTTGCACATCTGAAATGATTTACATAACCCACCTTTTGGAAGA
upper sequence: GLYMA02G33340.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G090747_T02 (Zea mays), 3'ss of exon 3
aatgctaattcttgttctcttccttttgtttagtattactagtggcaaatgggaaagtttgactgtgacaataggaacctgccttgtttcatttccacagCTTACACTTATTTTCTTATTATTGTCAGGAATGGTAGCAGCCCTTACCAATGAGAGTGCTACCAGCAAATCTGTATACTTTGCACACTGCACATCAGAGA----------------------------
| | | ||| | ||| || | | | |||||| || |||| | ||||| || || | | |||| || | |||| |||||||| || || ||||| |||||||| |||||||||||||| |||||||||| |||||||| ||||
-----------------------gtgcagtgaactttattctatgcacatagcttggcgct-cagtgacacccccaagtagccta---tgatttcatcaatttgc-tgaacattctgatatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACTTTGCACTTTGCACATCTGAGATGATCTACATCACACACCTTCTGGAAGA
upper sequence: GLYMA02G33340.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G173195_T01 (Zea mays), 3'ss of exon 2
aatgctaattcttgttctcttccttttgtttagtattactagt--ggcaaatgggaaagtttgactgtgacaataggaacctgccttgtttcatttccacagCTTAC-ACTTATTTTCTTATTATTGT-CAGGAATGGTAGCAGCCCTTACCAATGAGAGTGCTACCAGCAAATCTGTATACTTTGCACACTGCACATCAGAGA----------------------------
|| | | | || | | || || || | | | | | | | | | || | | | || || | | | |||| || |||| ||||| || |||||||| ||||||||||| ||||||||||| ||||||||| ||| |||||||| || |
-------------------------------agcaaaatttgtacgctatatcgggtagcgc-attacatccagtgcctcacggtcagcctaatatatgtaccatattgctgaacatggtcttatcgtgcagGTATGGTGGCGGCCCTTACGAATGAGAGTGCAACCAGCAAATCAGTATACTTTTCACTTTGCACATCGGAAATGATATACATCACTCATCTTCTAGCACC
upper sequence: GLYMA02G33340.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
aatgctaattcttgttctcttccttttgtttagtattactagtggcaaatgggaaagtttgactgtgacaataggaacctgccttgtttcatttcca-cagCTTACACTTATTTTCTTATTATTGTCAGGAATGGTAGCAGCCCTTACCAATGAGAGTGCTACCAGCAAATCTGTATACTTTGCACACTGCACATCAGAGA----------------------------
|| ||| |||| || | || | | | | | | | | || || || | || || | || ||| |||| | || ||||||||||| ||||| | || || |||||||| || |||||||||||||| ||||| || ||||| |||||||
----------------------gacctgaggagtgctactcagaccacctaaccaactcagctagaggccct------ttcgcgagtaccagttttatcatatttctctaattctctttatgtt-tcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
upper sequence: GLYMA02G33340.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------------aatgctaattcttgtt-------ctcttccttttgtttagtattactagtggcaaa-tgggaaagtttgactgtgacaataggaacctgccttgtttcattt--ccacagCTTACACTTATTTTCTTATTATTGTCAGGAATGGTAGCAGCCCTTACCAATGAGAGTGCTACCAGCAAATCTGTATACTTTGCACACTGCACATCAGAGA----------------------------
||| || ||||| || | | | | || | | || | | | ||| | || | | | || || || |||| || | ||| | || ||| || ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| || ||||||||||
gtaagttgttatttctttatgatggtaatataatagagggatcattgtgcttgaagtttcatatatgagcatccttgtcagataaacttcagcaatgatctggttctcattttgacctactaggagaagaaaaccaaaatttaaaaatgttg--ttattggatttaatcaagagtctcacattttcactttgattttccagGAATGGTAGCAGCCCTGACCAATGAGAGTGCTACCAGCAAATCTGTATACTTTGCACATTGTACATCAGAGATGATCTTCATTACTCATTTGTTGGCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaatgggaaagtttgactgtgacaataggaacctgccttgtttcatttccacagCTTACACTTATTTTCTTATTATTGTCAGGAATGGTAGCAGCCCTTACCAATGAGAGTGCTACCAGCAAATCTGTATACTTTGCACACTGCACATCAGAGA
gtttgac putative branch site (score: 4)
ccttgtttcatttcc putative PPT
tttcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgctaattcttgttctcttccttttgtttagtattactagtggcaaatgggaaagtttgactgtgacaataggaacctgccttgtttcatttccacagCTTACACTTATTTTCTTATTATTGTCAGGAATGGTAGCAGCCCTTACCAATGAGAGTGCTACCAGCAAATCTGTATACTTTGCACACTGCACATCAGAGA
aatgcta
- - - - - - - - ctcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gactgtg
