Sequence
atgc intronic sequence ATGC exonic sequencegtgagtatctctcttcgttttcctttctgggtattgcttgattttgattagtcgtttctggagaagtgatctctgtcattggattggtgtttcatttgattgaattgatctgtataatttacatgttatctgtgttcatatgtcagCTTGCTGCTAGGATTGCTGTGTCGAATCTCCACAAGAACACTAAGAAGTCATTTTCTGAGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G21790.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 1
gtgagtatctctcttcgttttcctttctgggtattgcttgattttgattagtcgtttctggagaagtgatctctgtcattggattggtgtttcatttgattgaattgatctgtataatttacatgttatctgtgttcatatgtca-gCTTGCTGCTAGGATTGCTGTGTCGAATCTCCACAAGAACACTAAGAAGTCATTTTCTGAGAC
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gtgagtaacccaccccgaaatcctcctcccctctggccttggtttcagctctcctgtctgtc-------tgtctgtctttctgtctgtgctgacgtggggttggttgcccc------------tgttctctgtcgtgattcgtgaagCTGGCGGCGAGGATTGCTGTGTCGAACCTGCACAAGAACACAAAGAAGTCCTTCTCGGAGAC
upper sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 1
gtgagtatctctcttcgttttcctttctgggtattgcttgattttgattagtcgtttctggagaagtgatctct--gtcattggattggtgtttcatttgattgaattgatctgta--taatttaca-tgttatctgtgttcatatgtca-gCTTGCTGCTAGGATTGCTGTGTCGAATCTCCACAAGAACACTAAGAAGTCATTTTCTGAGAC
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----------------------------------------------gtgaggaacccaccgtgaaatccccccttggtttcaactctcatgtctgtctttgttgtcctgacgtggggttggtttcctctcttctctatcgtgattcgtgaagTTGGCGGCGAGGATTGCTGTGTCTAACCTGCACAAGAACACAAAGAAGTCCTTCTCGGAGAC
upper sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ20157 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtatctctcttcgttttcctttctgggtattgcttgattttgattagtcgtttctggagaagtgatctctgtcattggattggtgtttcatttgattgaattgatctgtataatttacatgttatctgtgttcatatgtcagCTTGCTGCTAGGATTGCTGTGTCGAATCTCCACAAGAACACTAAGAAGTCATTTTCTGAGAC
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------------------------------------------------------------------------gtaagctagaagctttttctcgtttg-ttctgcaagcctttttctttgtcagtttacttatagt--tttcacagCTTGCTGCCAGGATTGTTGTCTCGAATCTTCACAAGAAAACTAAAAAGTCCTTCTCAGAGAC
upper sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ14283 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtatctctcttcgttttcctttctgggtattgcttgattttgattagtcgtttctggagaagtgatctctgtca-ttggattggtgtttcatttgattgaattgatctgtataatttacatgttatctgtgttcatatgtcagCTTGCTGCTAGGATTGCTGTGTCGAATCTCCACAAGAACACTAAGAAGTCATTTTCTGAGAC
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--------------------------------------------------------------------------gtaagctagaagcttgttctcgtttgttctgcaagcctttttctttgtcagtttacttatagt--tttcacagCTTGCTGCCAGGATTGTTGTCTCGAATCTTCACAAGAAAACTAAAAAGTCCTTCTCAGAGACMapped 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|164055351|gb|ES173874.1|ES173874EST: TGCTGAAACTGCTGCTGCTATGACTTGTAACCATCCTGATTATGCATCT CTTGCTGCTAGGATTGCTGTGTCGAATCTCCAC
genomic: TGCTGAAACTGCTGCTGCTATGACTTGTAACCATCCTGATTATGCATCTgtgagtatct ... catatgtcagCTTGCTGCTAGGATTGCTGTGTCGAATCTCCAC
EST:
gi|116415267|gb|EG457859.1|EG457859EST: CTGCTGAAACTGCTGCTGCTATGACTTGTAACCATCCTGATTATGCATCT CTTGCTGCTAGGATTGCTGTGTCGAATCTCCACAAGAACACTAAGAAGTCA
genomic: CTGCTGAAACTGCTGCTGCTATGACTTGTAACCATCCTGATTATGCATCTgtgagtatct ... catatgtcagCTTGCTGCTAGGATTGCTGTGTCGAATCTCCACAAGAACACTAAGAAGTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttgattgaattgatctgtataatttacatgttatctgtgttcatatgtcagCTTGCTGCTAGGATTGCTGTGTCGAATCTCCACAAGAACACTAAGAAGTCATTTTCTGAGAC
aattgat putative branch site (score: 4)
tataatttacatgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtatctctcttcgttttcctttctgggtattgcttgattttgattagtcgtttctggagaagtgatctctgtcattggattggtgtttcatttgattgaattgatctgtataatttacatgttatctgtgttcatatgtcagCTTGCTGCTAGGATTGCTGTGTCGAATCTCCACAAGAACACTAAGAAGTCATTTTCTGAGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
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