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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtttgttgaatagccaagtaacattgtttgttttctctgatattatagactcaaatggtttagttatcttgcctctgatcttattaattcctttcagGAAGAGGCTCTTCCAGATGATAAATGATCTCCCAACCATTTTCGAGGTTGTAACTGGCAATGCAAAGCAATCCAAGGATCAATCTGCTAACCACAACAGT

Basic information

species Arabidopsis thaliana
transcript AT1G14510.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G14510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G00630.1 (Glycine max), 3'ss of exon 3
-catgtttgttgaa-tagccaagtaacattgtttg--ttttctctgatattatagactcaaatggtttagttatcttgcctctgatcttattaattcctttcagGAAGAGGCTCTTCCAGATGATAAATGATCTCCCAACCATTTTCGAGGTTGTAACTGGCAATGCAAAGCAATCCAAGGATCAATCTGCTAACCACAACAGT
  || ||  | ||| |    |   |    ||||     ||  |     ||| || | | |   ||||    ||  |      |||| |   |   |  || |||||| ||||| || ||||||||||||||||| ||||| || |||||  |||| ||||| | ||| | |||||| ||||||||| | |||  |||||||| |
gtatattactagaaatctttagaaagttgtgttaaaagttcatgcatgattttatatttaggaggttcttctaattaa----tgatttggatgtatatttacagGAAAAGGCTTTTTCAGATGATAAATGATCTGCCAACAATCTTCGAACTTGTGACTGGAAGTGCTAGGCAATCAAAGGATCAACCAGCTGCCCACAACAAT

upper sequence: AT1G14510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 3
catgtttgttgaatagccaagtaacattgtttgttttctctgatattatagactcaaatggtttagttat----cttgcctctgatcttatt---aattcc---tttcagGAAGAGGCTCTTCCAGATGATAAATGATCTCCCAACCATTTTCGAGGTTGTAACTGGCAATGCAAAGCAATCCAAGGATCAATCTGCTAACCACAACAGT---
           ||||   ||| || || |||| |||    |   |    | |   | | ||| |  | ||    | ||  ||| || | | |   |||| |   || |||||||||||| |||||||||||||| || || |||||||| || || ||||| || ||    |  ||||||   |  |||   |||| ||| |||||||     
----------taatactgaagaaatatggtttctttaaagttcaaaaccaaatctagaaggtcttttgatactccatgattctaatttcaatcgaaattgcaatttacagGAAGAGGCTTTTCCAGATGATAAACGAGCTTCCAACCATATTTGAAGTTGTGACAGGA---GTTAAGCAACAAAGAGATATGTCTGGTAATCACAACAACAGC
















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|124773064|gb|EH863193.1|EH863193
EST:     ACGTTTCGGATTTGGCAAGAATGAGAG                         GAAGAGGCTCTTCCAGATGAATAAATGATCTCCCAACCATTTTCGAGGTTG
genomic: ACGTTTCGGATTTGGCAAGAATGAGAGgtaagtttct ... ttcctttcagGAAGAGGCTCTTCCAGATGA-TAAATGATCTCCCAACCATTTTCGAGGTTG
EST: gi|125221309|gb|EL235394.1|EL235394
EST:     TCTGTTGCATTTTACTTTGGTGCACGTTTCGGATTTGGCAAGAATGAGAG                         GAAGAGGCTCTTCCAGATGATAAAT
genomic: TCTGTTGCATTTTACTTTGGTGCACGTTTCGGATTTGGCAAGAATGAGAGgtaagtttct ... ttcctttcagGAAGAGGCTCTTCCAGATGATAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatagactcaaatggtttagttatcttgcctctgatcttattaattcctttcagGAAGAGGCTCTTCCAGATGATAAATGATCTCCCAACCATTTTCGAGGTTGTAACTGGCAATGCAAAGCAATCCAAGGATCAATCTGCTAACCACAACAGT
                                       tattaat  putative branch site (score: 2)
                                             ttcctttc  CT-rich tract
                                 tgatcttattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtttgttgaatagccaagtaacattgtttgttttctctgatattatagactcaaatggtttagttatcttgcctctgatcttattaattcctttcagGAAGAGGCTCTTCCAGATGATAAATGATCTCCCAACCATTTTCGAGGTTGTAACTGGCAATGCAAAGCAATCCAAGGATCAATCTGCTAACCACAACAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- tgtttgt
- - - - - - - - -caagtaa
- - - - - - - - - - - - - - - - - -ttctctg
- - - - - - - - - - - - - - - - - - - - - - - - - -actcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttag