Sequence
atgc intronic sequence ATGC exonic sequence...atggtcttctttttaaagtaaatattactatctgctatctcacaccggccacatcgtccttatcaatctttttgctgaactaaaatcatgttgttttcagGAAGAGGATAAGGCAAGGTTGGTGCAAGAAACTGGGTTGCAATTAAAGCAGATTAATAACTGGTTTATCAATCAAAGGAAGAGGAATTGGCACAGCAATC
Basic information
species | Glycine max |
transcript | GLYMA17G32980.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G32980.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 4
atggtcttctttttaaagtaaatattactatctgctatctcacaccggccacatcgtccttatcaatctttttgctgaactaaaatcatgttgttttcagGAAGAGGATAAGGCAAGGTTGGTGCAAGAAACTGGGTTGCAATTAAAGCAGATTAATAACTGGTTTATCAATCAAAGGAAGAGGAATTGGCACAGCAATC
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---gtatgtcagctca--cagataccattatcaggccttcc--------tgcatttccttttctaccactgatgctcatgtt---tcttaacctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATC
upper sequence: GLYMA17G32980.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 4
atggtcttctttttaaagtaaatattactatctgctatctcacaccggccacatcgtccttatcaatctttttgctgaactaaaatcatgttgtt--ttcagGAAGAGGATAAGGCAAGGTTGGTGCAAGAAACTGGGTTGCAATTAAAGCAGATTAATAACTGGTTTATCAATCAAAGGAAGAGGAATTGGCACAGCAATC
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--------gtatgtgacactacggcgac-atataat-tccctcgtcaacttttgctatcagcttgggttcattgctgatccactctttgcttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC
upper sequence: GLYMA17G32980.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 5
atggtcttctttttaaagtaaatattactatctgctatctcacaccggccacatcgtccttatcaatctttttgctgaactaaaatcatgttgtt--ttcagGAAGAGGATAAGGCAAGGTTGGTGCAAGAAACTGGGTTGCAATTAAAGCAGATTAATAACTGGTTTATCAATCAAAGGAAGAGGAATTGGCACAGCAATC
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------------gtacgtgacaccgcgtcaacttaattccctcgttagcttctgctatcaggttcggctcattgatgagcaactctttgcttactcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggccacatcgtccttatcaatctttttgctgaactaaaatcatgttgttttcagGAAGAGGATAAGGCAAGGTTGGTGCAAGAAACTGGGTTGCAATTAAAGCAGATTAATAACTGGTTTATCAATCAAAGGAAGAGGAATTGGCACAGCAATC
aactaaa putative branch site (score: 2)
ttgttttc putative PPT
ttatcaatcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atggtcttctttttaaagtaaatattactatctgctatctcacaccggccacatcgtccttatcaatctttttgctgaactaaaatcatgttgttttcagGAAGAGGATAAGGCAAGGTTGGTGCAAGAAACTGGGTTGCAATTAAAGCAGATTAATAACTGGTTTATCAATCAAAGGAAGAGGAATTGGCACAGCAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA