Sequence
atgc intronic sequence ATGC exonic sequence...gtggaaaaatcagggtcacgtttctaagaagcacacaacatgtatatatccgtacgttgatgcatatactgtgtaccagatttaataaatatctgtgcagTGTGGAACGAGCTAGAGAAAGAAAACAAGGAGTTTTTCGAGGAGTATGCCAAAGGTAAGAGTAAAGAAGACCGAATGTCGGAGGAAGAGACAACCCAAAT
Basic information
species | Glycine max |
transcript | GLYMA18G52240.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G52240.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G108723_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------gtggaaaaatcagg---gtcacgtttctaaga---agcacacaacatgtatatatccgtacgttgatgcatatactgtgtacc--agatttaataaatatctgtgcagTGTGGAACGAGCTAGAGAAAGAAAACAAGGAGTTTTTCGAGGAGTATGCCAAAGGTAAGAGTAAAGAAGACCGAATGTCGGAGGAAGAGACAACCCAAAT---
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gtaccggccgtactaccgtgcatatatactggacacgcgcacgcgttatgctttccttcccccgttcaaccatttctcgtttaccttccatgcataatatgcttcaataatcgatcatagattatattgttgttgttctattctatcatttcatgtggtctgaaaaagcacaccacatgcatgcagTGTGGAAGGAGCTAGAGAAAGAGAACAAGGAGTTCTTCGAGACGTACAACAAGGACC---GCGAGGAGCGGAAGGTGGAGGCGGAGACGATGGCGCGGATCGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatccgtacgttgatgcatatactgtgtaccagatttaataaatatctgtgcagTGTGGAACGAGCTAGAGAAAGAAAACAAGGAGTTTTTCGAGGAGTATGCCAAAGGTAAGAGTAAAGAAGACCGAATGTCGGAGGAAGAGACAACCCAAAT
atttaat putative branch site (score: 4)
agatttaataaatatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggaaaaatcagggtcacgtttctaagaagcacacaacatgtatatatccgtacgttgatgcatatactgtgtaccagatttaataaatatctgtgcagTGTGGAACGAGCTAGAGAAAGAAAACAAGGAGTTTTTCGAGGAGTATGCCAAAGGTAAGAGTAAAGAAGACCGAATGTCGGAGGAAGAGACAACCCAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- -gaaaaat
- - - - - - - - - - - - - - - -cacacaa
- - - - - - - - - - - - - - - - - - - catgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtac