Sequence
atgc intronic sequence ATGC exonic sequence...tccttgctcaagaagttaagggttcatgtaagattaatgtcaacaacatatttgactgtttattttttgctttgatttccaaagaatatttgttcaacagGCATAGGTGGACTGGTAGATATGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
Basic information
species | Glycine max |
transcript | GLYMA01G40380.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 2
--------tccttgctcaagaagttaagggttcatgtaagattaatgtcaacaacatatttgactgtttattttttgctttgatttc---caaagaatatttgttcaa--cagGCATAGGTGGACTGGTAGATATGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
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gtagtagctagcagcgccata-gtgacagacacctctcgccaccatgccgccatggcttccacct--tcacagcttcacttaacctcaagtaaaaaaaccttgtaaaaagcagGCATAGGTGGACTGGGAGATATGAGGCACACCTCTGGGACAACAGCTGCAAGAAGGAAGGCCAGACCAGAAAAGGACGCCAAG
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 2
-tccttgctcaagaagttaagggttcatgtaagattaatgtcaacaacatatttgactgtttattttttgctttgatttccaaagaatatttgttcaacagGCATAGGTGGACTGGTAGATATGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
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tgtattgatgaggcacctactcttttgtttttgagcaaatcatttgaccctttttatattgaatgacgaaggtttgtgtgtgtttgat-tcactggagcagGCACAGGTGGACTGGAAGATATGAAGCCCACCTCTGGGATAACAGTTGCAAAAAGGATGGACAGACAAGGAAGGGAAGGCAAG
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G146688_T01 (Zea mays), 3'ss of exon 2
-----------------tccttgctcaagaagttaagggttcatgtaagattaatgtcaacaacatatttgactgtttattttttgctttgatttccaaagaatatttgttcaacagGCATAGGTGGACTGGTAGATATGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
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gtacgtacgtacacgccgccgtgtcgagctagttgactggtc-cgtccgcccgtc--cgtccatggagctgaa-gctgaagttgaaactaaaactaaaactgaaagtaattaagcagGCATAGGTGGACGGGGAGGTATGAGGCGCACCTGTGGGACAACAGCTGCAAGAAGGAAGGCCAGAGCAGGAAGGGCCGGCAAG
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G021573_T02 (Zea mays), 3'ss of exon 1
tccttgctcaagaagttaagggttca---tgtaagattaatgtcaacaacatatttgactgtttattttttgctttgatttccaaagaatatttgttcaacagGCATAGGTGGACTGGTAGATATGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
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tgtctgtt--agggccaaacagttcagactgtttgaaccgcgactgttttatactgaatgatggagggttttgtttgtgttggattggat-tcactggagcagGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 2
-tccttgctcaagaagttaagggttca---tgtaagattaatgtcaacaacatatttgactgtttattttttgctttgatttccaaagaatatttgttcaacagGCATAGGTGGACTGGTAGATATGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
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ctctgtctgttagggccaaacagttcagactgtttgaaccgcgactgttttatactgaatgatggagggttttgtttgtgttggattggat-tcactggagCAGGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G028151_T01 (Zea mays), 3'ss of exon 2
----------------------tccttgctcaa--gaagttaagggttcatgtaagat-taatgtcaacaacatatttgactg-----tttattttttgctttgatttccaaagaatatttgttcaacagGCATAGGTGGACTGGTAGATATGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
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gtatcctcccaactcccgaccgtccgtacgccgtcgctgtcgcaggcgcgcgcgacccgcagcatccggcgcccgtgcgatcgagtcgctcactggccgcgtggtttcccaccgtgcaaa-----agcagGCATAGGTGGACGGGGAGGTATGAGGCGCACCTCTGGGACAACAGCTGCAGGAAGGAAGGGCAGACCCGGAAAGGCCGGCAAG
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
tccttgctcaagaagttaagggttcatgtaagattaatgtcaacaacatatttgactgt--ttatt--ttttgctttgatttccaaagaatatt-tgttcaacagGCATAGGTGGACTGGTAGATATGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
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--------------gttgtttttttatttta---taatattaa-actttgtttgactttcgttagtaatgttacatatacttacttaaaaggttatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 2
---tccttgctcaagaagttaagggttcatgtaagattaatgtcaacaacatatttgactgtttattttttgctttgatttccaaagaatatttgttcaacagGCATAGGTGGACTGGTAGATATGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
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gtgtttttttccctcatgtttcccccttttgccttccttgttttcctatcacatctttaccttctttttttttttctttttcctg---ttttatgtctatcagGCATAGATGGACAGGTAGATATGAAGCTCATCTATGGGACAACAGTTGCAAGAAAGAAGGGCAAAGCAGGAAAGGAAGGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatatttgactgtttattttttgctttgatttccaaagaatatttgttcaacagGCATAGGTGGACTGGTAGATATGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
tttgttc CT-rich tract
tttattttttgcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccttgctcaagaagttaagggttcatgtaagattaatgtcaacaacatatttgactgtttattttttgctttgatttccaaagaatatttgttcaacagGCATAGGTGGACTGGTAGATATGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
-ccttgct
- - - - - - - - - - - - catgtaa
- - - - - - - - - - - - - - - - - - - - caacaac
- - - - - - - - - - - - - - - - - - - - - - - - - -ttgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaaga