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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctactatatgttatttgtgttccttttaatgccctcttaggtttgagaattcttagttaatttgttttttttttatatgcagATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATTGTTCGTTTCAAGACTT

Basic information

species Arabidopsis thaliana
transcript AT3G50670.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G50670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G113592_T03 (Zea mays), 3'ss of exon 4
gtaatctactatatgttatttgtgttccttttaatgccctcttaggtttgagaattcttagttaatttgttttttttttatatgcagATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATTGTTCGTTTCAAGACTT
|||      ||     |  |      ||  ||| |      ||| | |||  |   | |  ||  | || |||  ||||||  |||||||||||  | | ||| || ||||||||||||||||||||||| ||| | || ||| | ||||||
gtacgtccttagggcatggtgtcaccccaattattttaaagttatggttgtaataacatcattgttctgatttggttttat--gcagATGACCCACAAAGTGACCCCAATGCTACTGGAGATCCATACAAAACACTCTTTGTTGCTAGACTT

upper sequence: AT3G50670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G38120.1 (Glycine max), 3'ss of exon 4
gtaatctactatatgttatttgtgttccttttaatgccctcttaggtttgagaattcttagt--taatttgttttttttttatatgcagATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATTGTTCGTTTCAAGACTT
|| ||      ||| ||    |||    |  ||||    || |   |||| |   |||   |   | | |  | ||   || ||||||||||| ||  ||||||| |||||||   | ||||||||||||||||||||||| ||  | | ||| 
gtgatgagtcctatatt----gtgaatttgctaatatt-tcatgattttgtgttctctggatgccattcttatattggcttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC

upper sequence: AT3G50670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G07200.2 (Glycine max), 3'ss of exon 4
gtaatctactatatgttatttgtgttccttttaatgccctcttaggtttgagaattcttagt--taatttgttttttttttatatgcagATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATTGTTCGTTTCAAGACTT
|| ||      ||| ||    | |    |  ||||    || |   |||  |   |||   |   | | |  | ||   || ||||||||||| ||  ||||||| |||||||   | ||||||||||||||||||||||| ||  | | ||| 
gtgatgagtcctatatt----gcgaatttgctaatatt-tcatgattttatgttctctggatgccattcttatattggcttctatgcagATGATCCACATAATGACCCAAATGTGTCGGGAGATCCATACAAGACATTGTTTGTGGCTAAACTC

upper sequence: AT3G50670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0023g01580.t01 (Vitis vinifera), 3'ss of exon 4
-------------------gtaatctactatatgttatttgtgttccttttaatgccctcttaggtttgagaattcttagt----taatttgttttttttttatatgcagATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATTGTTCGTTTCAAGACTT
                    |   ||| ||| || | | |  ||   ||||  |  ||  ||   | | |  ||| || ||    |  |||     | | || ||||||||||| || |||||||| ||||||  | | ||||| ||||||||||||||||| ||  | || |||
gtgataagctattttctccctctcctagtatttggtgtctaggtggattttg-tatccattttattatcaacatttttggtgccttgctttacacgtatcttctatgcagATGATCCAAATAATGACCCAAATATTTCGGGAGACCCATACAAGACATTGTTTGTAGCTAGGCTT

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|164155614|gb|EL971157.1|EL971157
EST:     GGAGAAAGGTGTTGAAAAGGCTGCTTGAGGACTTAAAGAAAT                         ATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATTGT
genomic: GGAGAAAGGTGTTGAAAAGGCTGC-TGAGGACTTAAAGAAATgtaatctact ... ttatatgcagATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATTGT
EST: gi|116473966|gb|EG516558.1|EG516558
EST:     ATTGCGACTGGAGAAAGGTGTTGAAAAGGCTGCTGAGGACTTAAAGAAAT                         ATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATCGT
genomic: ATTGCGACTGGAGAAAGGTGTTGAAAAGGCTGCTGAGGACTTAAAGAAATgtaatctact ... ttatatgcagATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATTGT
EST: gi|116473967|gb|EG516559.1|EG516559
EST:     ATTGCGACTGGAGAAAGGTGTTGAAAAGGCTGCTGAGGACTTAAAGAAAT                         ATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATCGT
genomic: ATTGCGACTGGAGAAAGGTGTTGAAAAGGCTGCTGAGGACTTAAAGAAATgtaatctact ... ttatatgcagATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATTGT
EST: gi|163977429|gb|ES119787.1|ES119787
EST:     ATTGCGACTGGAGAAAGGTGTTG-AAAGGCTGCTGAGGACTTAAAGAAAT                         ATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACA
genomic: ATTGCGACTGGAGAAAGGTGTTGAAAAGGCTGCTGAGGACTTAAAGAAATgtaatctact ... ttatatgcagATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACA
EST: gi|164122182|gb|ES188361.1|ES188361
EST:     GGAGAAAGGTGTTGAAAAGGCTGCTGAGGACTTAAAGAAAT                         ATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATTGT
genomic: GGAGAAAGGTGTTGAAAAGGCTGCTGAGGACTTAAAGAAATgtaatctact ... ttatatgcagATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATTGT
EST: gi|164161859|gb|ES161427.1|ES161427
EST:     ATTGCGACTGGAGAAAGGTGTTG-AAAGGCTGCTGAGGACTTAAAGAAAT                         ATGACCCCAAATAATGATCCAAATGCTACTGGAGATCCATACAAGACA
genomic: ATTGCGACTGGAGAAAGGTGTTGAAAAGGCTGCTGAGGACTTAAAGAAATgtaatctact ... ttatatgcagATGACCCC-AATAATGATCCAAATGCTACTGGAGATCCATACAAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgccctcttaggtttgagaattcttagttaatttgttttttttttatatgcagATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATTGTTCGTTTCAAGACTT
                                 tttgttttttttttat  CT-rich tract
              tttgagaattcttagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctactatatgttatttgtgttccttttaatgccctcttaggtttgagaattcttagttaatttgttttttttttatatgcagATGACCCCAATAATGATCCAAATGCTACTGGAGATCCATACAAGACATTGTTCGTTTCAAGACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC