Sequence
atgc intronic sequence ATGC exonic sequence...ggtatagttatatatatatatatatatatatatatatatatatatatatatttatatacatgtaaatatgatagtattggtgtgttgttgatttttgcagCCTCCATACACAGCTCCACAATACACTGAGGAGTTTGATTTTGAGGCCATGAATGAAAAGTTCAAAAAAGATGAAGTATGGGGTTCTCTTGGAAAGACAA
Basic information
species | Glycine max |
transcript | GLYMA01G35640.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
--ggtatagttatatatatatatatatatatatatatatatatatatatatattta-tatacatgtaaatatgatagtattggtgtgt-tgttgatttttgcagCCTCCATACACAGCTCCACAATACACTGAGGAGTTTGATTTTGAGGCCATGAATGAAAAGTTCAAAAAAGATGAAGTATGGGGTTCTCTTGGAAAGACAA
| | ||| || | | ||||| ||| | ||| | || | ||| || || ||| || || | || || ||||| |||||||| | | | ||| || | | ||||| || |||||||| |||||||||||| ||||| || ||||||||||| |||||| |||||| |||| |
ttgatcatgtttcatgtttttatatgattatgatgctgcttattaaagagcatctggtattgattgaagtat--taatacttttgagtctgttg--ttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT
upper sequence: GLYMA01G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G051622_T02 (Zea mays), 3'ss of exon 5
ggtatagttatatatatatatatatatatatatatatatatatatatatatttatatacatgtaaatatgatagt-attggtgtgt-tgttgatttttgcagCCTCCATACACAGCTCCACAATACACTGAGGAGTTTGATTTTGAGGCCATGAATGAAAAGTTCAAAAAAGATGAAGTATGGGGTTCTCTTGGAAAGACAA
| || || |||| | | || || | || | |||| | || || | | ||| | | | | | || ||| | | | ||||||| | || | ||| || || |||||| || |||||||| |||||||||||| ||||| || ||||||||||| |||||| ||||||||||| |
-gagtatttgtataccttgggaaatg-atgcttggattgaataatatttgttgttaaatagttaagtgtcagatttgttaatgtttgtatcttcctttgcagTTTTCACAGTCAGTAACAACATTCACTGAAGAATTTGATTTCACGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGAAAGAAAT
upper sequence: GLYMA01G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G132796_T01 (Zea mays), 3'ss of exon 5
ggtatagttatatatatatatatatatatatatatatatatatatatatatttatatacatgtaaatatgatagt-attggtgtgt-tgttgatttttgcagCCTCCATACACAGCTCCACAATACACTGAGGAGTTTGATTTTGAGGCCATGAATGAAAAGTTCAAAAAAGATGAAGTATGGGGTTCTCTTGGAAAGACAA
| ||| | |||| | | || || | ||| ||||| || | | ||||| | | | | ||| ||| | | | ||||||| | || | | | || || |||||| || |||||||| |||||||||||| ||||| || ||||||||||||||||| |||||| |||| |
-gagggagtatttgtataccttgggaaatgatgctaggattgaata-atattgttaaatagttaaatgtcagatttgttgatgtttgtatcttgctttgcagTTTTCACAGTCTGTAACAGCATTCACTGAAGAATTTGATTTCACGGCCATGAATGAGAAGTTTAACAAAGATGAAGTATGGGGCCATCTTGGTAAGAAAT
upper sequence: GLYMA01G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G341027_T01 (Zea mays), 3'ss of exon 5
---ggtatagttatata-tatatatatatatatatatatatatatatatatatatttatatacatgtaaatatgatagtattggtgtgttgttgatttttgcagCCTCCATACACAGCTCCACAATACACTGAGGAGTTTGATTTTGAGGCCATGAATGAAAAGTTCAAAAAAGATGAAGTATGGGGTTCTCTTGGAAAGACAA
|| | | | | | | | | | || | | | | || | | |||| |||| || ||| || | | | |||| | | | | | | ||| ||||| |||||||| ||| |||||||| |||||||| ||||||||||||||||| |||||| || | ||
cttaaaatgcctctgttctgttttcagtcccttgaggacattctttgttgtcgacttgcttttttttaaact--gtagtcttcac-tgtcattc-tctctacagCAATCGCATCCCATAACCAAGTTCACAGAGGACTTTGATTTCATGGCAATGAATGAGAAGTTCAACAAAGATGAAGTATGGGGCCATCTTGGTAAAAGAA
upper sequence: GLYMA01G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G45330.1 (Arabidopsis thaliana), 3'ss of exon 4
ggtatagttatatatatatatatatatatata-tatatatatatat-atatatttatatacatgtaaatatgatagtattggtgtgttgttgattt-ttgcagCCTCC-ATACACAGCTCCAC-----AATACACTGAGGAGTTTGATTTTGAGGCCATGAATGAAAAGTTCAAAAAAGATGAAGTATGGGGTTCTCTTGGAAAGACAA
|| | |||| || | | | | | | | | ||| | | | | |||| || | | | | || | | | | ||| | || | |||||| ||| || | || || | | |||||||| || ||||||||||| || |||||||| |||||||| || |||| ||||||||| ||||||||
ggaagtgttaaattcaaagcattgcaactttggtttgtatccttttcacacatttcactatttctca-tttgtt--tttcctttggttctaaatgtgttgcagTCTCGGATCCCTAGTTCTAGCATTGAGTACACTGAAGAATTTGATTTTGAAGCAATGAATGAGAAGTTCAAGAAGAGTGAACTATGGGGTTATCTTGGAA------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatatttatatacatgtaaatatgatagtattggtgtgttgttgatttttgcagCCTCCATACACAGCTCCACAATACACTGAGGAGTTTGATTTTGAGGCCATGAATGAAAAGTTCAAAAAAGATGAAGTATGGGGTTCTCTTGGAAAGACAA
tgttgat putative branch site (score: 4)
tttttgc CT-rich tract
tttatatacatgtaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtatagttatatatatatatatatatatatatatatatatatatatatatttatatacatgtaaatatgatagtattggtgtgttgttgatttttgcagCCTCCATACACAGCTCCACAATACACTGAGGAGTTTGATTTTGAGGCCATGAATGAAAAGTTCAAAAAAGATGAAGTATGGGGTTCTCTTGGAAAGACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtg