Sequence
atgc intronic sequence ATGC exonic sequencegtaggcccttgtgtgtcttatgtgtttgttcagcttagattcactctggtatatgtgattctttaatccttcaaatgtttggagatgtttcagGAGCTTCATAGTGCAAGATCTACATTTGAGCAAGCTCGGTTTAATCTG
Basic information
species | Glycine max |
transcript | GLYMA18G51810.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 7
gtaggcccttgtgtgtcttatgtgtttgttcagcttagattcactctggtatat--gtgattctttaatccttcaaatgtttggagatgtttcagGAGCTTCATAGTGCAAGATCTACATTTGAGCAAGCTCGGTTTAATCTG
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gtatgttcct-tctatcatttgtcttcat---atttgtatttagaaagttggatcactgcatccttactaatttatatgtcacacaac----cagGAGCTCCATAGTGCCAGATCCTCATTTGAGCAAGCTCGTTTCAACCTG
upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM5G872204_T01 (Zea mays), 3'ss of exon 4
gtaggcccttgtgtgtcttatgtgtttgttcagcttagattcactctggtatatgtgattctttaatccttca--aatgtttggagatgtttcagGAGCTTCATAGTGCAAGATCTACATTTGAGCAAGCTCGGTTTAATCTG
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gtaaaaaccattcttattcaacatttcacagtgttaacacaaattaaggcatctctccctcccccttaactaaatagcatttgataataac-cagGAGCTTCACAGTGCTAGATCTTCATTTGAGCAAGCTCGTTTCAACCTG
upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------------------------------gtaggcccttgtgtgtcttatgtgtttg--ttcagcttagattcactctggtatatgtgattctttaatccttcaaatgtttggagatgtttcagGAGCTTCATAGTGCAAGATCTACATTTGAGCAAGCTCGGTTTAATCTG
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gtgttgttcaatgttaatttgaaagtgatattatccatttttggctgagcaagtgatgtatctagtcattctgacatatatgattccagaagagtttgtattgcatatctgtgttttttaaattctaatgtagtttagtgatactccagGAGCTTCATAATGCAAGATCTACATTTGAGCAAGCTCGCTTTAATCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcactctggtatatgtgattctttaatccttcaaatgtttggagatgtttcagGAGCTTCATAGTGCAAGATCTACATTTGAGCAAGCTCGGTTTAATCTG
ctttaat putative branch site (score: 4)
attctttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggcccttgtgtgtcttatgtgtttgttcagcttagattcactctggtatatgtgattctttaatccttcaaatgtttggagatgtttcagGAGCTTCATAGTGCAAGATCTACATTTGAGCAAGCTCGGTTTAATCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT