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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggaattgatgactttttccatctaatcgaggtgtggctttgaatgaagctctgtgtcttatctgattttatttattttttttgcctacagGATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCAGAACACTTTACTGAGCGTATGGCGCGGATGAAAGAAGATCCAGAGTTGA

Basic information

species Arabidopsis thaliana
transcript AT4G35450.1
intron # 4
splice site 3'
intron type U2

Mapped 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|86041554|gb|DR337309.1|DR337309
EST:     ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAG                         GATCCACAAATGTCTCCTTTTTTGGGATGCTTTCTCG
genomic: ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTCTCCTTTTTTGG-ATGCTTTCTCG
EST: gi|125313398|gb|EL327483.1|EL327483
EST:     CCCTGACTTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAG                         GATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAAT
genomic: CCCTGA-GTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAAT
EST: gi|86041556|gb|DR337311.1|DR337311
EST:     ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAG                         GATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCA
genomic: ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCA
EST: gi|124929305|gb|EL006863.1|EL006863
EST:     CCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAG                         GATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCA
genomic: CCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCA
EST: gi|86041557|gb|DR337312.1|DR337312
EST:     ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAG                         GATCCACAAATGTCTCCTTTTTTGGAT
genomic: ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTCTCCTTTTTTGGAT
EST: gi|125327642|gb|EL341722.1|EL341722
EST:     CGCCTTAGTTCAG                         GATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCA
genomic: CGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCA
EST: gi|86041567|gb|DR337322.1|DR337322
EST:     ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAG                         GATCCACAAATGTCTCCTTT
genomic: ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTCTCCTTT
EST: gi|125074191|gb|EL138233.1|EL138233
EST:     ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAG                         GATCCAACAAATGTCTCCTTTTTTGGATGCTTTCTCG
genomic: ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCA-CAAATGTCTCCTTTTTTGGATGCTTTCTCG
EST: gi|125275455|gb|EL289540.1|EL289540
EST:     CCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAG                         GATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCA
genomic: CCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCA
EST: gi|86041568|gb|DR337323.1|DR337323
EST:     ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAG                         GATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTG
genomic: ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTG
EST: gi|125181418|gb|EL197647.1|EL197647
EST:     AAACTTGGTACCGCCTTAGTTCAG                         GATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCA
genomic: AAACTTGGTACCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCA
EST: gi|164099224|gb|ES190737.1|ES190737
EST:     ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAG                         GATCCACAAATGTCTCCTTTTTTAGGTATGCTTTCTCGAATCCTGAAACAG
genomic: ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTCTCCTTTTTT-GG-ATGCTTTCTCGAATCCTGAAACAG
EST: gi|125164529|gb|EL191226.1|EL191226
EST:     ACCCTGACTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAG                         GATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAAT
genomic: ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAAT
EST: gi|125325848|gb|EL339928.1|EL339928
EST:     CCGCCTTAGTTCAG                         GATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCA
genomic: CCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCA
EST: gi|86041544|gb|DR337299.1|DR337299
EST:     ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAG                         GATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAAC
genomic: ACCCTGAGTTTAAGACAATGGCCGAGAAACTTGGTACCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAAC
EST: gi|124795445|gb|EH885124.1|EH885124
EST:     TGGCCGAGAAACTTGGTACCGCCTTAGTTCAG                         GATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCA
genomic: TGGCCGAGAAACTTGGTACCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCA
EST: gi|124994228|gb|EL066497.1|EL066497
EST:     TTGGTACCGCCTTAGTTCAG                         GATCCACAAATGTCTTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGC
genomic: TTGGTACCGCCTTAGTTCAGgttaggaatt ... ttgcctacagGATCCACAAATGTC-TCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttgaatgaagctctgtgtcttatctgattttatttattttttttgcctacagGATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCAGAACACTTTACTGAGCGTATGGCGCGGATGAAAGAAGATCCAGAGTTGA
                        atctgat  putative branch site (score: 4)
                              ttttatttattttttt  CT-rich tract
                  tgtcttatctgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaggaattgatgactttttccatctaatcgaggtgtggctttgaatgaagctctgtgtcttatctgattttatttattttttttgcctacagGATCCACAAATGTCTCCTTTTTTGGATGCTTTCTCGAATCCTGAAACAGCAGAACACTTTACTGAGCGTATGGCGCGGATGAAAGAAGATCCAGAGTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG