Sequence
atgc intronic sequence ATGC exonic sequence...atttgcatttttcttttgtttctttggaacatactaatcccaaacagctgactggattctatatttttggctaattttttcttcaaccttacactcacagGGAAAAGGAAAAGTAAAGTTCCCTCCTGCAGCACGAAGAATGGATACTCTTAATGATTTATTAGCTGCAAGTGACCTTATATCACTCCATTGTGCTTTAA
Basic information
species | Glycine max |
transcript | GLYMA18G47240.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G476107_T02 (Zea mays), 3'ss of exon 2
------atttgcatttttcttttgtttctttggaacat--actaatcccaaac--agctgactggattctatatttttggctaattttttcttcaaccttacactcacagGGAAAAGGAAAAG-------TAAAGTTCCCTCCTGCAGCACGAAGAATGGATACTCTTAATGATTTATTAGCTGCAAGTGACCTTATATCACTCCATTGTGCTTTAA
| |||||||| |||| | | | | | | | || || |||| ||| |||| | | || | || | | | || ||| | | | |||||| |||||||| | |||||||| ||||| |||||||||||||| || ||||||||||| || |
tctccaacttgcatttctcttccttctgtacccattttgaataagatgtaagttaagaatactgctttcaatatcctgactt--cttgcacatccgctgaagGCAAGTGGGAAAACAAAGCGGCCTTCTATTGTTTTCCCTTCTGCAGCAAGGAGAATGGACACTCTCAATGATTTATTAGCAGCGAGTGACCTTATTTCGC---------------
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G418294_T01 (Zea mays), 3'ss of exon 1
atttgcatttttcttttgtttctttggaacatactaatcccaaacagctgactggattctatatttttg-----gctaattttttcttca--accttacactcacagGGAAAAGGAAAAGTA--------AAGTTCCCTCCTGCAGCACGAAGAATGGATACTCTTAATGATTTATTAGCTGCAAGTGACCTTATATCACTCCATTGTGCTTTAA
|| | || | ||| || | || || | | | | | | | || |||| | || | ||||| | || | | | | || |||||| || || || ||| |||| ||| |||||||||||||||| |||||| ||||||| |||||||| || | || |
cttcatggtgtttctgggttactggcacatgtaatattggcgatgaagttaaagcatgatatagatctgaccttgttaattgtaatgacattatgtgaagGTTACTGGGAAAGTAAAGCGTCCTTCTATTGTATTTCCTTCTGCTGCAAGAAGAATGGATACTCTCAATGATCTATTAGCAGCAAGTGATCTAGTTTCGC---------------
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 1
atttgcatttttcttttgtttctttggaacatactaatcccaaacagctgactggattctatatttttggctaattttttcttcaaccttacactca-cagGGAAAAGGAAAAGTAAA------------GTTCCCTCCTGCAGCACGAAGAATGGATACTCTTAATGATTTATTAGCTGCAAGTGACCTTATATCACTCCATTGTGCTTTAA
||||||| | | | ||| | | ||| ||| ||| | | | ||| | | | |||| | |||| || | | |||||||| |||||| ||| || ||||| || || ||||||||||||||||| ||||||||| | ||||||||||||||| | || || |
-tttgcatctaaatgtgttttgaccagcatatattaagtatttgttcttgaaaatcatgcagaatttggattgaattttgtctaaaccaaccatttaacagGGAAAGGGAAAATTAAGCAGATCTATTACATTTCCTCCAGCTGCCCGAAGAATGGATACTCTCAATGATTTACTCGCTGCAAGTGACCTTGTTTCCCTTC------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctgactggattctatatttttggctaattttttcttcaaccttacactcacagGGAAAAGGAAAAGTAAAGTTCCCTCCTGCAGCACGAAGAATGGATACTCTTAATGATTTATTAGCTGCAAGTGACCTTATATCACTCCATTGTGCTTTAA
accttac putative branch site (score: 3)
tatatttttggctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttgcatttttcttttgtttctttggaacatactaatcccaaacagctgactggattctatatttttggctaattttttcttcaaccttacactcacagGGAAAAGGAAAAGTAAAGTTCCCTCCTGCAGCACGAAGAATGGATACTCTTAATGATTTATTAGCTGCAAGTGACCTTATATCACTCCATTGTGCTTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- -tgcattt
- - - - - - - - - - - - - - - - - - - -ccaaaca
- - - - - - - - - - - - - - - - - - - - - - - gctgact