Sequence
atgc intronic sequence ATGC exonic sequence...tacctactttagaagaaaaaaatgttattctggaatccatatttgcttttgcatggatttttccgtaactaatgtcaaaaatggattcaatatggcttagGTATACTGTGGGGAAGATTACCCCAATACAGAGACGAGAAGTTCGAGCATCAGATTTTGGTCCTAGAGCAAGCTTTTGGATGAATTTTCCTAAAGAAGGT
Basic information
species | Glycine max |
transcript | GLYMA10G06800.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 2
tacctactttagaagaaaaaaatgttattc--tggaatccatatttgcttttgc-atggatttttccgtaactaatgtcaaaaatgga---ttcaatatggcttagGTATACTGTGGGGAAGATTACCCCAATACAGAGACGAGAAGTTCGAGCATCAGATTTTGGTCCTAGAGCAAGCTTTTGGATGAATTTTCCTAAAGAAGGT
| | | | | | ||||| | ||||| | || | | | |||| || | || ||||| | | || | |||||||| || || || ||||| || ||||| || | ||| |||||||| || ||||||||||| || |||||||| || |||||||| || || ||||||||
-----gatcctgcaacgtacatttttatttaattaaatccgaagttatgatggttacagattgtttta-agtatatttcaaaccggcaatgttttgttgtacttagGTACACAGTTGGAAAGATCACACCAATTCAAAAACGTGAAGTTCGTGCTTCAGATTTTGGACCAAGAGCAAGTTTCTGGATGAACTTCCCAAAAGAAGGA
upper sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------------------tacctactttagaagaaaaaaatgttattc-tggaatccatatt----tgcttttgcatggatttttccgtaactaatgtcaaaaatggattcaatatggcttagGTATACTGTGGGGAAGATTACCCCAATACAGAGACGAGAAGTTCGAGCATCAGATTTTGGTCCTAGAGCAAGCTTTTGGATGAATTTTCCTAAAGAAGGT
| | ||| | | | | | | || | |||||| | || || || | ||| || | | || ||||| || | |||||||| || || ||||||||||| ||||| || | ||| ||||||| || ||||||||||| || | |||||| || ||||||||||| | ||||||||
gtatgaactaatgcagtagtggttagttggttactgcattagtttcttactggctccaagcttgcaacctgcacttttcgtgttaggaactgctagcttctgcaacgtacattttctttaattaaatccagggtatgatgtttacagattgttttaggtatatttgaaatcggcaatggtttt--ttgtacttagGTACACAGTTGGGAAGATTACACCAATTCAAAAACGTGAAGTTCATGCTTCAGATTTTGGACCAACAGCAAGTTTCTGGATGAATTTCTCAAAAGAAGGA
upper sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 1
-tacctactttagaagaaaaaaatgttattctggaatccatatttgcttttgcatggatttttccgtaactaatgtcaaaaatgga-ttcaatatggcttagGTATACTGTGGGGAAGATTACCCCAATACAGAGACGAGAAGTTCGAGCATCAGATTTTGGTCCTAGAGCAAGCTTTTGGATGAATTTTCCTAAAGAAGGT
|| |||| | || |||| | | | | || ||| | || || ||| | | | || | ||| | || ||| || | || |||||||||||||| ||||| ||||||||||| ||||| ||||| ||||||||||||||||| ||||| || |||||||||| ||||| ||||||||
aggcccacttgtcatatcaaggatgtaaatatatgctg-atctttatgtctgtcattatattttactcatgattgctgagtatgaaattgaatgtga-tcagATATACTGTGGGGAAAATTACACCAATACAGAGGCGAGAGGTTCGTGCATCAGATTTTGGTCCCAGAGCCAGTTTTTGGATGAGCTTTCCAAAAGAAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttgcatggatttttccgtaactaatgtcaaaaatggattcaatatggcttagGTATACTGTGGGGAAGATTACCCCAATACAGAGACGAGAAGTTCGAGCATCAGATTTTGGTCCTAGAGCAAGCTTTTGGATGAATTTTCCTAAAGAAGGT
aactaat putative branch site (score: 2)
attcaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacctactttagaagaaaaaaatgttattctggaatccatatttgcttttgcatggatttttccgtaactaatgtcaaaaatggattcaatatggcttagGTATACTGTGGGGAAGATTACCCCAATACAGAGACGAGAAGTTCGAGCATCAGATTTTGGTCCTAGAGCAAGCTTTTGGATGAATTTTCCTAAAGAAGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - -aaaaaaa
- - - - - - - - - - - - - attctgg
- - - - - - - - - - - - - - - - - - - - - - - - - gcatgga