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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAGAGGAGgtattcaccatatttattagcattattaatgacaccacaaaatcatatataaagaatagccctgttgaaatagtttacataattctcgcctgtttcctgttttctctag

Basic information

species Arabidopsis thaliana
transcript AT5G04740.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G04740.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv13s0147g00220.t01 (Vitis vinifera), 5'ss of exon 7
ATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAGAGGAGgtattcaccatattt---attagcattattaatgacaccacaaaatcata--tataaagaatagccctgttgaaatagtttacataattctcgcctgtttcctgttttctctag
 ||||||| ||| | ||||||||||||||||| ||||| ||||| ||||||||||||||  || |  | ||   ||| | ||   |  |  ||     |     ||    | ||   |  || | || |       | |||      |  |  ||               
CTTGATGTTGATGTTGCAACTCATATACATGTCAAAGATGATGGGCCAAAGAGGAGgtacgcaactgacttgtgattggaatggcttttagcattgttatgctttagtcgttaatgttgtcctttttaattctaccttcatgtaagccaacacttg--------------
















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|86079610|gb|DR375367.1|DR375367
EST:     GTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAGAGGAG                         CCTGCTTGTCATAGAGACAGCGGACAGGCCAGGTCTTGTCGTAGAGATGAT
genomic: GTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAGAGGAGgtattcacca ... ttttctctagCCTGCTTGTCATAGAGACAGCGGACAGGCCAGGTCTTGTCGTAGAGATGAT
EST: gi|124912677|gb|EH986672.1|EH986672
EST:     GTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAGAGGAG                         CCTGCTTGTCATAGAGA
genomic: GTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAGAGGAGgtattcacca ... ttttctctagCCTGCTTGTCATAGAGA
EST: gi|164225840|gb|ES168808.1|ES168808
EST:     ATGGACCAAAGAGGAG                         CCTGCTTGTCATAGAGACAGCGGACAGGCCAGGTCTTGTCGTAGAGATGAT
genomic: ATGGACCAAAGAGGAGgtattcacca ... ttttctctagCCTGCTTGTCATAGAGACAGCGGACAGGCCAGGTCTTGTCGTAGAGATGAT
EST: gi|124814227|gb|EH899093.1|EH899093
EST:     GTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAGAGGAG                         CCTGCTTGTCATAGAGACAGCGGACAG
genomic: GTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAGAGGAGgtattcacca ... ttttctctagCCTGCTTGTCATAGAGACAGCGGACAG
EST: gi|116403963|gb|EG446555.1|EG446555
EST:     GTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAGAGGAG                         CCTGCTTGTCATAGAGACAGCGGACAGGCCAGGTCTTGTCGTAGAGATGAT
genomic: GTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAGAGGAGgtattcacca ... ttttctctagCCTGCTTGTCATAGAGACAGCGGACAGGCCAGGTCTTGTCGTAGAGATGAT
EST: gi|125010476|gb|EL082745.1|EL082745
EST:     GTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAGAGGAG                         CCTGCTTGTCATAGAGAC
genomic: GTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAGAGGAGgtattcacca ... ttttctctagCCTGCTTGTCATAGAGAC
EST: gi|86082088|gb|DR377847.1|DR377847
EST:     GTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAGAGGAG                         CCTGCTTGTCATAGAGACAGCGGACAGGCCAGGTCTTGTCGTAGAGATGAT
genomic: GTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAGAGGAGgtattcacca ... ttttctctagCCTGCTTGTCATAGAGACAGCGGACAGGCCAGGTCTTGTCGTAGAGATGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAGAGGAGgtattcaccatatttattagcattattaatgacaccacaaaatcatatataaagaatagccctgttgaaatagtttacataattctcgcctgtttcctgttttctctag

- - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG