Sequence
atgc intronic sequence ATGC exonic sequence...gacatatcaataatttaatttggcattattttttcttgtgtaaggtgctattgcctattcgtttgaataaaaaatacttacgctattcatcttgagatagGTCAGTCATCACCCAATGATTGTTGCATGCCATTGTGAGGGAAAAGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
Basic information
species | Glycine max |
transcript | GLYMA04G38330.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0031g02980.t01 (Vitis vinifera), 3'ss of exon 5
gacatatcaataatttaatttggcattattttttcttgtgtaaggtgc-tattgcctattcgtttgaataaa--aaatacttacgctat--tcatcttgagatagGTCAGTCATCACCCAATGATTGTTGCATGCCATTGTGAGGGAAAAGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
| | | || | || || | | | || | | | |||| | | | | | ||||| |||| || | ||||||| |||||| ||||| ||||| |||||||||||||||||||||||||| | || |||||| | ||||| |||||||| ||||||||||||| ||||| ||||| |
-----actagtggttggctcccttttttttaatatatatatatgctccatattattttattggtaatactggttaaataattacacttcggttatcttgatatagGTTAGTCACCACCCTATGATTGTTGCATGCCATTGTGAGGGTCATGGTTGGAAACTATGGGGAGACAGCAACCTAAAAAGTAAATTCTGGGGCCGTTCTA
upper sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------------------------------------------------------gacatatcaataatttaatttgg---cattattttt-tcttgtgtaaggtgctattgcctattcgtttgaataaa----aaatactta--cgctattcatcttgagatagGTCAGTCATCACCCAATGATTGTTGCATGCCATTGTGAGGGAAAAGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
|| || | | | ||| | || | || | | | |||| | | | || || | ||| | || | ||| |||| || | |||| || ||||| ||||||||||| ||||| || || ||||| | ||||||||||||||||||||||||||| || ||||| || |||||||| ||||| |
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
upper sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 3'ss of exon 5
-gacatatcaataatttaatttggcattat-tttttcttgtgtaaggtgctattgcctattcgtttgaataaaaaatacttacgctattcatcttgagatagGTCAGTCATCACCCAATGATTGTTGCATGCCATTGTGAGGGAAAAGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
|| |||| ||| | | | || | |||| | | || | || | | | | | | || | | | | | |||| |||||||| ||||||||||| ||||| ||||| ||||| | |||||||||||| ||||||||||||||||| ||||| || ||||||||||||||||
ggagatattaatttgcaacctctttgtcatatctttcgagctttagat--taagtaaaagttaatcatcttgcatcttctatctccctacgttgctttgcagGTGAGTCATCATCCAATGATTGTGGCATGTCATTGCGAGGGCAGAGGCTGGAAATTCTGGGGTGACAGCAATTTGAAAAGCAAGTTTTGGGGTCGTTCAA
upper sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S427_40V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------gacatatcaataatttaatttggcattattttttcttgtgtaaggtgctattgcctattcgtttgaataaaaaatacttacgctattc-atcttgagat--agGTCAGTCATCACCCAATGATTGTTGCATGCCATTGTGAGGGAAAAGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
| | | | || | ||| | | | ||| | | ||||| |||| || | |||| | || || | | || | ||| | |||| || |||||||||||||| || ||||| || || ||||| ||| |||||||| ||||| |||||||| || ||||| || |||||||||||||| |
gtttgacgcgattgtcattttctattgtttgacaatctcttaggagtctgatggaattgccacatttgttcgcgccgagatgtt--tctggtacttgtgcttcatctctaagga---attgtaggttggactgaactataattatctgaaatcctctgttttgcggcgcagGTGAGCCATCACCCAATGATCGTGGCATGTCACTGCGAGGGTCGAGGATGGAAATTCTGGGGAGACAGCAACTTGAAAAGCAAGTTTTGGGGTCGTTCTA
upper sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
-----gacatatcaataatttaatttggcattattttttcttgtgtaaggtgctattgcctattcgtttgaataaaaaatacttacgctattcatcttgag-atagGTCAGTCATCACCCAATGATTGTTGCATGCCATTGTGAGGGAAAAGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
|||| || | | || | ||| || | || | ||| ||| || | || | | | | | | |||| | || | | ||||||||||||| ||||||||||||||||||||||| ||||| | ||| |||| ||| |||||||||||||| || ||||| || |||||||| ||||| |
ctttaaacatttcga-acttcag---aacataatatgagctaat-taatttgc-atcttccatctctacgtgtttttatttttatttttatttttattttgtacagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
upper sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ15167 (Selaginella moellendorffii), 3'ss of exon 5
gacatatcaataatttaatttggcattattttttcttgtgtaaggtgctattgcctattcgtttgaataaaaaatacttacgctattcatcttgagatagGTCAGTCATCACCCAATGATTGTTGCATGCCATTGTGAGGGAAAAGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
|| || | | || | || || || | | ||| ||| | |||||||||| || || ||| | || || || || ||||||||| || |||||| | ||||| ||||||||| |||| |||||||||||||| |||||||
---------------------------------------gttagccagtcagtttttttttctctgctacttgatgctgattttcttcgtct--gtacagGTCAGTCACCATCCCATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA
upper sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 6
gacatatcaataatttaatttggcattattttttcttgtgtaaggtgctattgcctattcgtttgaataaaaaatacttacgctattcatcttgagatagGTCAGTCATCACCCAATGATTGTTGCATGCCATTGTGAGGGAAAAGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
|| || | | || || | || ||||| | | ||| ||| | |||||||||| || |||||| | || || || || ||||||||| || |||||| | ||||| ||||||||| |||| |||||||||||||| |||||||
---------------------------------------gttagcta--gtcagcttttttctctgctacttgatactgattttcttcgtct--gtacagGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctattgcctattcgtttgaataaaaaatacttacgctattcatcttgagatagGTCAGTCATCACCCAATGATTGTTGCATGCCATTGTGAGGGAAAAGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
tacttac putative branch site (score: 1)
ttcatctt putative PPT
tattcgtttgaataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gacatatcaataatttaatttggcattattttttcttgtgtaaggtgctattgcctattcgtttgaataaaaaatacttacgctattcatcttgagatagGTCAGTCATCACCCAATGATTGTTGCATGCCATTGTGAGGGAAAAGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
- catatca
- - - - - - - - - - -ggcatta
- - - - - - - - - - - - - - - - -tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - gctattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctattca