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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccatctcttctcatgattcaatccaaagattgtctctttttgttttgttatgcaattgttcaataaagagattgtctttttgtttagGCGAGGAAAGATGCTACACAAGTTGTTGCAAATCTTCAGAGGCAACAAGTCAATTCACGTCTTATTGCTGCTGATTATCTTGAATCCAACATTGATCTTA

Basic information

species Arabidopsis thaliana
transcript AT4G17270.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G17270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G066051_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------gtaccatctcttctcatg-attcaatccaaagattgtctctttttgttttgttatgcaa----ttgttcaataaagagattgtctttttgttt-----------agGCGAGGAAAGATGCTACACAAGTTGTTGCAAATCTTCAGAGGCAACAAGTCAATTCACGTCTTATTGCTGCTGATTATCTTGAATCCAACATTGATCTTA
                                             | |  | || || | |   |   ||| || |       | || | |||||   |   ||    |  | || |     |  ||| | | |  ||           || | |||||||||||||| ||||||||||||||  | || || || |||||    |||    |  | ||  |||| || || || || || |  |||||  
gtatgtaatttgacctgtttttgcatgtagattgacagtactactggagtagcttttattacatacataatacatacccctcttgttatcgtttttacacaaaaaaactgatacattcgtatggatgtatctctacttctgattgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTATCCTCAAAGATAGTAGCGTCTGAGTACCTAGAGTCAAATAAAGATCTCT

upper sequence: AT4G17270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G351417_T01 (Zea mays), 3'ss of exon 2
gtaccatctcttctcatgattcaatccaaagattgtctctttttgttttgttatgcaattg------ttcaataaagagat-tgtctttttgttt-----agGCGAGGAAAGATGCTACACAAGTTGTTGCAAATCTTCAGAGGCAACAAGTCAATTCACGTCTTATTGCTGCTGATTATCTTGAATCCAACATTGATCTTA
 || ||  | || | | ||    |   |     |  ||  |  | |||    |   || ||      |   ||  |   || | |  ||||| ||     || | |||||||||||||| ||||||||||||||  | || || ||||||||    |||    |  ||||  |||| || || || || || |  |||||  
-tatcaagtatt-tgaagaccggagggagtacctcccttgtcctttttacacaaaaaactgatacattcttatggatgtatctctacttttgattgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAACAAGTATCCTCAAAGATAGTTGCATCTGAGTACCTAGAGTCAAATAAAGATCTCT
















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|124841583|gb|EH926020.1|EH926020
EST:     TGCTCACTTCTCTTCCTAATTTGAACTTGGAG                         GCGAGGAAAGATGCTACACAAGTTGTTGCAAATCTTCAG
genomic: TGCTCACTTCTCTTCCTAATTTGAACTTGGAGgtaccatctc ... ttttgtttagGCGAGGAAAGATGCTACACAAGTTGTTGCAAATCTTCAG
EST: gi|86070914|gb|DR366671.1|DR366671
EST:     CTGATACTCTTCGCCGTTTGCTCACTTCTCTTCCTAATTTGAACTTGGAG                         GCGAGGAAAGATGCTACACAAGTTGTTGCAAATCTTCAGAGGCAACAAGTC
genomic: CTGATACTCTTCGCCGTTTGCTCACTTCTCTTCCTAATTTGAACTTGGAGgtaccatctc ... ttttgtttagGCGAGGAAAGATGCTACACAAGTTGTTGCAAATCTTCAGAGGCAACAAGTC
EST: gi|116482972|gb|EG525564.1|EG525564
EST:     CTGATACTCTTCGCCGTTTGCTCACTTCTCTTCCTAATTTGAACTTGGAG                         GCGAGGAAAGATGCTACACAAGTTGTTGCAAATCTTCAGAGGCAACAAGTC
genomic: CTGATACTCTTCGCCGTTTGCTCACTTCTCTTCCTAATTTGAACTTGGAGgtaccatctc ... ttttgtttagGCGAGGAAAGATGCTACACAAGTTGTTGCAAATCTTCAGAGGCAACAAGTC
EST: gi|86070913|gb|DR366670.1|DR366670
EST:     CTGATACTCTTCGCCGTTTGCTCACTTCTCTTCCTAATTCGAACTTGGAG                         GCGAGGAAAGATGCTACACAAGTTGTTGCAAATCTTCAGAGGCAACAAGTC
genomic: CTGATACTCTTCGCCGTTTGCTCACTTCTCTTCCTAATTTGAACTTGGAGgtaccatctc ... ttttgtttagGCGAGGAAAGATGCTACACAAGTTGTTGCAAATCTTCAGAGGCAACAAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctttttgttttgttatgcaattgttcaataaagagattgtctttttgtttagGCGAGGAAAGATGCTACACAAGTTGTTGCAAATCTTCAGAGGCAACAAGTCAATTCACGTCTTATTGCTGCTGATTATCTTGAATCCAACATTGATCTTA
                                       ttgtctttttgttt  CT-rich tract
     ttttgttttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccatctcttctcatgattcaatccaaagattgtctctttttgttttgttatgcaattgttcaataaagagattgtctttttgtttagGCGAGGAAAGATGCTACACAAGTTGTTGCAAATCTTCAGAGGCAACAAGTCAATTCACGTCTTATTGCTGCTGATTATCTTGAATCCAACATTGATCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT