Sequence
atgc intronic sequence ATGC exonic sequencegtgagttcccttcatatttaaaggtttgctccttttttggggtcttggtttacttgttgttagtactgcagattggttttgtttgttgttattggaagatggtgagggtataagtagttattggcgtttcagtgatgttgatgggatagacaatgtttcattgttttgcagTGATTGTAGGGGAAATTGCCAATTTTGCTGCTTATGCCTTTGCGCCTGCCATTTTAGTAACTCCTCTTGGTGCTCTCAGCATAATTATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G34470.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G34470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 2
gtgagttcccttcatatttaaaggtttgctccttttttggggtcttggtttacttgttgttagtactgcagattggttttgtttgttgttattggaagatggtgagggtataagtagttattggcgtttcagtgatgttgatgggatagacaatgtttcattgttttgcagTGATTGTAGGGGAAATTGCCAATTTTGCTGCTTATGCCTTTGCGCCTGCCATTTTAGTAACTCCTCTTGGTGCTCTCAGCATAATTATCAG
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----------------------------------------------------------tctaatatactgaagttactgtttcatttgtttttagacaa-----aaaatgtcactaaggaaagaaacttgactaatg--------gcatcttacatgacctttgtgaacagTGATTGTGGGAGAAATTGCAAATTTTGCTGCTTATGCATTTGCTCCTGCTATTCTTGTTACTCCTCTTGGGGCACTCAGTATAATCATCAG
upper sequence: AT1G34470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G129268_T01 (Zea mays), 3'ss of exon 2
gtgagttcccttcatatttaaaggtttgctccttttttggggtcttggtttacttgttgttagtactgcagattggttttgtttgttgttattggaagatggtgagggtataagtagttattggcgtttcagtgatgttgatgggatagaca-atgtttcattgttttg--cagTGATTGTAGGGGAAATTGCCAATTTTGCTGCTTATGCCTTTGCGCCTGCCATTTTAGTAACTCCTCTTGGTGCTCTCAGCATAATTATCAG
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-------------------------------------------------------------------------tgcacagaactgctgctac-aaccttttttaggagaacatgttactgaagctttctgaatgaaagaaacttgaaatatgtacgtacatgtgttttgtacagTGATTGTAGGTGAAATTGCTAATTTTGCTGCTTATGCATTCGCTCCTGCTATTCTTGTCACTCCTCTTGGTGCACTCAGTATAATCATCAG
upper sequence: AT1G34470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G104147_T02 (Zea mays), 3'ss of exon 2
gtgagttcccttcatatttaaaggtttgctccttttttggggtcttggtttacttgttgttagtactgcagattggttttgtttgttgttattggaagatggtgagggtataagtagttattggcgtttcagtgatgtt---gatgggatagacaatgtttcattgttttgcagTGATTGTAGGGGAAATTGCCAATTTTGCTGCTTATGCCTTTGCGCCTGCCATTTTAGTAACTCCTCTTGGTGCTCTCAGCATAATTATCAG
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-----------------------------------------------------------------------------------tgctactatcttttctaggagtacctgttactcaagctttctgaatgagagaaacttgaaatgtgttcacttacatgtcttttgtgcacagtgattgtagGTGAAATTGCTAATTTTGCTGCTTATGCATTCGCTCCAGCTATTCTTGTCACTCCTCTTGGTGCACTAAGTATAATCATAAG
upper sequence: AT1G34470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G104147_T03 (Zea mays), 3'ss of exon 2
gtgagttcccttcatatttaaaggtttgctccttttttggggtcttggtttacttgttgttagtactgcagattggttttgtttgttgttattggaagatggtgagggtataagtagttattggcgtttcagtgatgttgatgggatagacaatgtttcattgttttgcagTGATTGTAGGGGAAATTGCCAATTTTGCTGCTTATGCCTTTGCGCCTGCCATTTTAGTAACTCCTCTTGGTGCTCTCAGCATAATTATCAG
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------------------------------------------------------------caaaactgctgct--actatcttttctaggagtacctgttactcaagctttctg-aatgagagaaacttgaaatgtgttcac--------ttacatgtcttttgtgcacagTGATTGTAGGTGAAATTGCTAATTTTGCTGCTTATGCATTCGCTCCAGCTATTCTTGTCACTCCTCTTGGTGCACTAAGTATAATCATAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttattggcgtttcagtgatgttgatgggatagacaatgtttcattgttttgcagTGATTGTAGGGGAAATTGCCAATTTTGCTGCTTATGCCTTTGCGCCTGCCATTTTAGTAACTCCTCTTGGTGCTCTCAGCATAATTATCAG
tgttgat putative branch site (score: 4)
tttcatt putative PPT
attgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttcccttcatatttaaaggtttgctccttttttggggtcttggtttacttgttgttagtactgcagattggttttgtttgttgttattggaagatggtgagggtataagtagttattggcgtttcagtgatgttgatgggatagacaatgtttcattgttttgcagTGATTGTAGGGGAAATTGCCAATTTTGCTGCTTATGCCTTTGCGCCTGCCATTTTAGTAACTCCTCTTGGTGCTCTCAGCATAATTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC