Sequence
atgc intronic sequence ATGC exonic sequence...ttaagtgttcatgtaagagcaattccaacaacatatttgactgtttacttttattttttttatgttttgctttaatttctaaggaatgtttgttcatcagGCATAGGTGGACTGGTAGATACGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
Basic information
species | Glycine max |
transcript | GLYMA11G04910.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G04910.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 2
---ttaagtgttcatgtaagagcaattccaacaacatatttgactgt-ttacttttattttt---tttatgttttgctttaatttc---taaggaatgtttgttcat--cagGCATAGGTGGACTGGTAGATACGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
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gtagtagctagcagcgccatagtga--cagacacctctcgccaccatgccgccatggcttccaccttcacagcttcacttaacctcaagtaaaaaaaccttgtaaaaagcagGCATAGGTGGACTGGGAGATATGAGGCACACCTCTGGGACAACAGCTGCAAGAAGGAAGGCCAGACCAGAAAAGGACGCCAAG
upper sequence: GLYMA11G04910.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G021573_T02 (Zea mays), 3'ss of exon 1
ttaagtgttcatgtaagagcaattccaacaacata---tttgactgtttacttttattttttttatgttttgctttaatttctaaggaatgtttgttcatcagGCATAGGTGGACTGGTAGATACGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
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-tgtctgttagggccaaa-cagttcagactgtttgaaccgcgactgttttatactgaatgatggagggttttgtttgtgttggattggat-tcactggagcagGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
upper sequence: GLYMA11G04910.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 2
--ttaagtgttcatgtaagagcaattccaacaacata---tttgactgtttacttttattttttttatgttttgctttaatttctaaggaatgtttgttcatcagGCATAGGTGGACTGGTAGATACGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
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ctctgtctgttagggccaaa-cagttcagactgtttgaaccgcgactgttttatactgaatgatggagggttttgtttgtgttggattggat-tcactggagCAGGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
upper sequence: GLYMA11G04910.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G146688_T01 (Zea mays), 3'ss of exon 2
--------ttaagtgttcatgtaa-gagcaattccaacaacatatttgactgtttacttttattttt----tttatgttttgctttaatttctaaggaatgtttgttcatcagGCATAGGTGGACTGGTAGATACGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
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gtacgtacgtacacgccgccgtgtcgagctagttgactggtccgtccgcccgtccgtccatggagctgaagctgaagttgaaactaaaactaaaactgaaagtaattaagcagGCATAGGTGGACGGGGAGGTATGAGGCGCACCTGTGGGACAACAGCTGCAAGAAGGAAGGCCAGAGCAGGAAGGGCCGGCAAG
upper sequence: GLYMA11G04910.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
ttaagtgttcatgtaagagcaattccaacaacatatttgactgtttacttttattttttttatgttttgctttaatttctaaggaatgtttgttcatcagGCATAGGTGGACTGGTAGATACGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
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---gttgtttttttatt-----ttataatattaaactt---tgtttgacttt-cgttagtaatgttaca-tatacttacttaaaaggttatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
upper sequence: GLYMA11G04910.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 2
-----ttaagtgttcatgtaagagcaattccaacaacatatttgactgtt-tacttttattttttttatgttttgctttaatttctaaggaatgtttgttcatcagGCATAGGTGGACTGGTAGATACGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
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gtgtttttttccctcatgtttcccccttttgccttccttgttttcctatcacatctttaccttctttttttttttcttt--ttcctg----ttttatgtctatcagGCATAGATGGACAGGTAGATATGAAGCTCATCTATGGGACAACAGTTGCAAGAAAGAAGGGCAAAGCAGGAAAGGAAGGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacttttattttttttatgttttgctttaatttctaaggaatgtttgttcatcagGCATAGGTGGACTGGTAGATACGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
ctttaat putative branch site (score: 4)
tttgttc putative PPT
ttattttttttatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaagtgttcatgtaagagcaattccaacaacatatttgactgtttacttttattttttttatgttttgctttaatttctaaggaatgtttgttcatcagGCATAGGTGGACTGGTAGATACGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - -catgtaa
- - - - - - - - - - - - ccaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaatgt