Sequence
atgc intronic sequence ATGC exonic sequence...catacagcaattgcatgatcacaccacacctctaattccattcttgagttgcaattaattttcttgtaaaggggagtttctgcttgttcaatggttgtagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAATATGAACTTGACAAGAAGACAGGATTGATTAAG
Basic information
species | Glycine max |
transcript | GLYMA03G42280.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 3
-------catacagcaattgcatgatcacaccacacctctaattccattcttgagttgcaattaattttcttgtaaaggggagtttctgcttgttcaatggttgtagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAATATGAACTTGACAAGAAGACAGGATTGATTAAG
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attgttctgtttaacgattctagaa----gctttatctacagtcggttcctgacagtgcatgcaacctacatggttaatgg--cttccatttatatcaca-ccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG
upper sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
-catacagcaattgcatgatcacaccacacctctaattccattcttgagttgcaattaattttcttgtaaaggggagtttctgcttgttcaatggttgtagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAATATGAACTTGACAAGAAGACAGGATTGATTAAG
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gtaagcatcgtgttcataat-atatttgtcatcaaattgaag-caaacactgcgatttatttcaggatgcatctggacctg-acatgttttttt-ttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
upper sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 3
-catacagcaattgcatgatcacaccacacctctaattccattcttgagttgcaattaattttcttgtaaaggggagt-ttctgcttgttcaatggttgtagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAATATGAACTTGACAAGAAGACAGGATTGATTAAG
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ttgttgaggaaaaataagtgcatggtttttttttaattacgatatttaacaa-atctagttagctccaaacaatgaccgcgttatataattttttatt-cagGTTGTTGAGATCACAAAGGGAAGCAAAGTCAAATACGAGCTTGACAAGAAAACTGGACTGATTAAG
upper sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 3
catacagcaattgcatgatcacaccacacctctaattccattcttgagttg--caattaattttcttgtaaaggggagtttctgcttgttcaatggttgtagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAATATGAACTTGACAAGAAGACAGGATTGATTAAG
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-atttgcttgtcgagcaaaaa-agtgcattttttatcataatgtttaacaaatctactagttcgcttcatacagtgactgcattatttacatctttatgcagGTTGTTGAGATCACAAAGGGAAGCAAAGTTAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG
upper sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 3
catacagcaattgcatgatcacaccacacctctaattccattcttgagttgcaattaattttcttgtaaaggggagtttctgcttgttcaatggttgtagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAATATGAACTTGACAAGAAGACAGGATTGATTAAG
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------gtaagttttttcctactctttgt-tctaaacagagtat---gttgttattagattctcta-----atcattttatctttggatgattatt--agGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagttgcaattaattttcttgtaaaggggagtttctgcttgttcaatggttgtagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAATATGAACTTGACAAGAAGACAGGATTGATTAAG
aattaat putative branch site (score: 3)
aattaattttcttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catacagcaattgcatgatcacaccacacctctaattccattcttgagttgcaattaattttcttgtaaaggggagtttctgcttgttcaatggttgtagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAATATGAACTTGACAAGAAGACAGGATTGATTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
catacag
- - - - - - gcatgat
- - - - - - - - - - - -ccacacc
- - - - - - - - - - - - - - - - - - -ccattct
- - - - - - - - - - - - - - - - - - - - - - - agttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgct