Sequence
atgc intronic sequence ATGC exonic sequencegtaccatttgattatgattacggttacctgttgtcactggtttaattgatatgtatgaacaagctcttatgctcatgacagGAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTTGGCTCTACACCTGAGATGTTTAAGAAGAACTTGATATGGGTTGTCACTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G08510.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g43090.4 (Oryza sativa), 3'ss of exon 3
----------gtaccatttgattatgattacggttacc---------tgttgtcactggtttaattgatatgtatgaacaagctcttatgctca---tgacagGAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTTGGCTCTACACCTGAGATGTTTAAGAAGAACTTGATATGGGTTGTCACTC
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gtaagtggttgcacattctgtttttagtttcatttctcatttcagcattttgttatagattcgtatgtctctttcaagctggcaattatttaaaattttgcagGAAACGGCTCTTAACCATGTAAGGACTGCTGGTCTTCTTGGAGATGGTTTTGGGGCTACACCGGAGATGAGCAAACGGAACTTGATATGGGTTGTCAGCA
upper sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G079308_T01 (Zea mays), 3'ss of exon 9
gtaccatttgattatgattacggttacctgttgtcactggtttaattgatatgtatgaacaagctcttatgctcatgacagGAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTTGGCTCTACACCTGAGATGTTTAAGAAGAACTTGATATGGGTTGTCACTC
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gtaaggatttgttacatttgaggtgtgagattgttgtggctgaggattggac-tatgaaaaagtttggat--ttgatccagGAAACGGCACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTCGGCTCCACACCAGAGATGAGTAAACGGAACTTATTCTGGGTGGTTAGCC
upper sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G406603_T02 (Zea mays), 3'ss of exon 2
---gtaccatttgattatgattacg-gttacctgttgtcactggtttaattgatatgtatgaacaagctcttatgctcatgacagGAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTTGGCTCTACACCTGAGATGTTTAAGAAGAACTTGATATGGGTTGTCACTC
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gtaaaatgatttgttaattttgaggtgtgagattttgtagctgag--gattgg-acg-atgaaaaagtttggat--ttgatccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTTGGCTCCACACCAGAGATGAGTAAACGAAACTTGTTCTGGGTGGTTAGCC
upper sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G23560.1 (Glycine max), 3'ss of exon 2
----------gtaccatttga--ttatgatt---acggttacctgttgtcactggtttaattgatatgtatgaacaagctcttatgctcatga------cagGAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTTGGCTCTACACCTGAGATGTTTAAGAAGAACTTGATATGGGTTGTCACTC
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aatgggaaaaacacctatggaaactaagttttgtacaattgcatattg--atttattttattttattgtttgaattgtttgtttatttaaaaaaacaaacagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGATTTGGTTCCACGCCTGAAATGTGTAAGAAGAACCTGATATGGGTGGTGACTA
upper sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G21910.1 (Glycine max), 3'ss of exon 2
--------------------gtaccatttgattatga-ttacggttacctg-ttgtcactggtttaattgatatgtatgaacaagctcttatgctcatgacagGAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTTGGCTCTACACCTGAGATGTTTAAGAAGAACTTGATATGGGTTGTCACTC
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atcaaagaacaatgccaaaaacacctatggaatctaagttttgtgcaattgcttattgatgattttattttattgcctaaattgtctgtt---ttccaaacagGAGACTGCACTTAATCATGTTAAGACTGCTGGGCTTCTTGGTGATGGATTTGGTTCCACGCCTGAAATGTGCAAAAAGAACCTGATATGGGTGGTGACTA
upper sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G08060.3 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------gtaccatttgattatgattacggtta----cctgttgtcactggtttaattgatatgtatgaacaagctcttatgctcatgacagGAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTTGGCTCTACACCTGAGATGTTTAAGAAGAACTTGATATGGGTTGTCACTC
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gtaagtccgtcctcatacaagtgaatctttatgatcttcagagatgagtatgctttgactaagatagggctgtttatttagtcactgtaattcaatttcatatatagataatatcattctgttgttacttttcatactatatttatatcaactatttgcttaacaacagGAAACTGCACTTAATCATGTTAAAAGTGCTGGGCTTCTTGGTGATGGCTTTGGTTCCACGCCAGAAATGTGCAAAAAGAACTTGATATGGGTGGTTACTCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|124838236|gb|EH922675.1|EH922675EST: TCATGAATCATCTGCAG GAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTT
genomic: TCATGAATCATCTGCAGgtaccatttg ... ctcatgacagGAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTT
EST:
gi|125232142|gb|EL246227.1|EL246227EST: TGAATCATCTGCAG GAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTT
genomic: TGAATCATCTGCAGgtaccatttg ... ctcatgacagGAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTT
EST:
gi|86073234|gb|DR368991.1|DR368991EST: ATCTATAGAAACCGTCATGAATCATCTGCAG GAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTT
genomic: ATCTATAGAAACCGTCATGAATCATCTGCAGgtaccatttg ... ctcatgacagGAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgttgtcactggtttaattgatatgtatgaacaagctcttatgctcatgacagGAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTTGGCTCTACACCTGAGATGTTTAAGAAGAACTTGATATGGGTTGTCACTC
aattgat putative branch site (score: 4)
tttaattgatatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccatttgattatgattacggttacctgttgtcactggtttaattgatatgtatgaacaagctcttatgctcatgacagGAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTTGGCTCTACACCTGAGATGTTTAAGAAGAACTTGATATGGGTTGTCACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC