Sequence
atgc intronic sequence ATGC exonic sequence...gttccttttattgaacatttccactatgaaatttaatttactttagtattcctttctcctttttgtttaattattcacatggaatcgacattaattgcagAACAAATGCAATGTGGGATATGCATTCATCAACATGATCAATCCTGGCTTGATTATACCATTCTATCAG
Basic information
species | Glycine max |
transcript | GLYMA08G28860.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 12
--------------gttccttttattgaacatttccactatgaaatttaatttactttagtattcctttctcctttttgtttaattattcacatggaatcgacattaattgcagAACAAATGCAATGTGGGATATGCATTCATCAACATGATCAATCCTGGCTTGATTATACCATTCTATCAG
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gtgagtggtctggtattagtcttggttagcagata-gttctttaattttacctgcttctttgttacttgca--tgtttgttggactaaacattaataatctccatt---ttcagAATAAGTGCAATGTTGGTTATGCATTCATCAACATGATCAATCCTGACAATATTGTTCCATTTTATAAG
upper sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 2
gttccttttattgaacatttccactatgaaatttaatttactttagtattcctttctcctttttgtttaatt-attcacatggaatcgacattaatt--gcagAACAAATGCAATGTGGGATATGCATTCATCAACATGATCAATCCTGGCTTGATTATACCATTCTATCAG
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------gtaagtaaatcttgcatggatggaatttctttggggaagaaaatcacatatggcatatgcacatctgattcacctttttacaaattctgttttacagAACAAATGCAATGTGGGCTATGCTTTTGTCAACATGATTGGTCCTCTTCATATTGTTCCATTACATCAG
upper sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S78_22V6.1 (Physcomitrella patens), 3'ss of exon 12
-----------------------------------------------------------------------gttccttttattgaacatttc----cacta--tgaaatttaatttacttta-gtattcctttctcctttttgtttaattattcacatg--gaatcgacat-taat-----tgcagAACAAATGCAATGTGGGATATGCATTCATCAACATGATCAATCCTGGCTTGATTATACCATTCTATCAG-------------------------------
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gtacgttgaccggcactgtgatgggttgagtatttggtagtggtcgggtggagcataggtgtgcattccaagtaggtttggggggacagaacgagacagtgggtgaggtgtggaggggggcacgtgtggggttgtgtttggtgcgaaggcgtgtgggtaacgaggtggcgcgtgatgggtgcgcagAACAAGTGCAATGTTGGGTATGCGTTCATCAACATGATGTCGCCGTCGCGCATAGTTCCGTTTTACAAGGCGTTCAACGGGAAGAAGTGGGAGAAGTTCA
upper sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ29695 (Selaginella moellendorffii), 3'ss of exon 7
gttccttttattgaacatttccactatgaaatttaatttactttagtattcctttctcctttttgtttaattattcacatggaatcgacattaattgcagAACAAATGCAATGTGGGATATGCATTCATCAACATGATCAATCCTGGCTTGATTATACCATTCTATCAG
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-------------------------------gtgattttaggcgagcaaaagtgtttccct--------ggtattgac-cggcttttgcct---gtgcagAATAAATGCAACGTTGGCTATGCATTCATCAACATGACCGAGCCAGCTCACATCGTCCCCTTTTACAAG
upper sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ28200 (Selaginella moellendorffii), 3'ss of exon 9
gttccttttattgaacatttccactatgaaatttaatttactttagtattcctttctcctttttgtttaattattcacatggaatcgacattaattgcagAACAAATGCAATGTGGGATATGCATTCATCAACATGATCAATCCTGGCTTGATTATACCATTCTATCAG
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-------------------------------gtgattttaggcgagcaaaagtgtttccctggtattgatcggcttttgcctg------------tgcagAACAAATGCAACGTTGGCTATGCATTCATCAACATGACCGAGCCAGCTCACATCGTCCCCTTTTACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtattcctttctcctttttgtttaattattcacatggaatcgacattaattgcagAACAAATGCAATGTGGGATATGCATTCATCAACATGATCAATCCTGGCTTGATTATACCATTCTATCAG
cattaat putative branch site (score: 3)
tttttgtttaattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttccttttattgaacatttccactatgaaatttaatttactttagtattcctttctcctttttgtttaattattcacatggaatcgacattaattgcagAACAAATGCAATGTGGGATATGCATTCATCAACATGATCAATCCTGGCTTGATTATACCATTCTATCAG
gttcctt
- - - - - - - - - ttccact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggaa