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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgatttagagggctttgtttggcaatatacttgtgggcatgtaaaatcattgaaaagcttttctgataacttcttttccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATACATGGAATGAGCCTCTTGGACGTGGAACCGAGATTAGATTACATCTTAGG

Basic information

species Arabidopsis thaliana
transcript AT4G24190.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 6
gtaagttgatttagagggctttgtttggcaatatacttgtgggcatgtaaaatcattgaaaagcttttctgataacttcttttccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATACATGGAATGAGCCTCTTGGACGTGGAACCGAGATTAGATTACATCTTAGG
|||||||      |  | |||| ||||   || |     |   | | |    |      |  |  |||  |      |  | | |  ||| || ||||| ||||||||||| ||| | ||    |||||| | |||||||||||||||||||| || ||||| |||||||||||||| |||||||||||  | 
gtaagttaccgctgctg-ctttttttgttcatttctcgttttacttatgtgcttgcctcacggtattttgg------tgctgtactcttttagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATACATGGAATGAACCCCTTGGCCGTGGAACCGAGATAAGATTACATCTGCGA

upper sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 6
gtaagttgatttagagggctttgtttggcaatatacttgtgggcatgtaaaatcattgaaaagcttttctgataacttcttttccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATACATGGAATGAGCCTCTTGGACGTGGAACCGAGATTAGATTACATCTTAGG
|||||    |   |   | ||| ||||   || |  |  |   | | |  | |  | |  |   | || || |      ||   |  ||| |||||||| ||||||||||| ||| | ||   ||||||  | || |||||||||||||||||||| ||||| |||||||| ||||| ||||| |||||  | 
gtaagacattgctggctgtttt-tttgttcatttcttgatttacctatttacttgt-gtcacattattgtggtg-----ttgcactcttttagGTATGTGTGGGAATCAAAAGCTGATGGATCATTTGCCATCTCTGAGGATACATGGAATGAGCCCCTTGGCCGTGGAACTGAGATAAGATTGCATCTGCGA

upper sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 6
gtaagttgatttaga---gggctttgtttggcaatatacttgtgggcatgtaaaatcattga----------aaagcttttctga-taactt-----cttttccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATACATGGAATGAGCCTCTTGGACGTGGAACCGAGATTAGATTACATCTTAGG
||||||   ||| ||   |   ||  ||| | |||    | ||    | | |||||  |||             | |    |||  ||||||      | ||  |||||||||||||||||||||||||| ||| | ||   ||| ||| |||| || |||||||||||||| || |||||||| ||||| |||||||||||||| || | |
gtaagtccttttggacctgatgttgtttttgtaatcagttagtattgaaggaaaatttttgtttgttgacttgtaacccagctgcctaacttgaaacttatttggttttcagGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATACATGGAATGAACCACTTGGACGAGGAACTGAGATTAGATTACACCTCAAG

upper sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 6
-gtaagttgatttagagggctttgtttggcaatatacttgtgggcatgtaaaatcattgaaaagcttttctgataacttcttttccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATACATGGAATGAGCCTCTTGGACGTGGAACCGAGATTAGATTACATCTTAGG
 ||||||   ||| ||   | |  | | |   | |  |||| | | |||||      |    | ||    ||| || |    ||| |||||||||||||||||||||||||| ||| | ||   ||||||  |||| || |||||||||||||| ||||| || |||||||| |||||||||||||| || |  
agtaagtctttttgga---cctgatatcgtttt-tgtttgttgacttgtaacccagct----atctgacttgaaaatta---ttcggttttcaGGTATGTATGGGAATCAAAAGCTGATGGAGCATTTGCAATTTCAGAAGATACATGGAATGAACCTCTAGGGCGTGGAACTGAGATTAGATTACACCTCAA-

upper sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 6
---gtaagttgatttagagggctttgtttggcaatatacttgtgggcatgtaaaatcattgaaaagcttt-tctgataacttcttttcc-----gttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATACATGGAATGAGCCTCTTGGACGTGGAACCGAGATTAGATTACATCTTAGG
     ||  ||| | |    | | ||  |  |  | | ||    |   |  ||   |  ||||  |   | ||||||   | | ||| |     | ||  ||| || | ||||| || || ||| | || || || || ||| | || ||||||  |||||||||||||||||||||||||||||||||| |  | || | |
tcctgaaaatgagtaatttaggtctgcctatctctgtgctct--gttgttcaactcctgtgaactgtggtgtctgatgggtgccttttccacatggttctagGCATATCTGGGAGTCTAACGCTGATGGAAACTTCGCCGTTACTGAAGATACAGAGAATGAGCCTCTTGGACGTGGAACCGAGATTAGAATTTACCTGAAG

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|163981094|gb|ES002996.1|ES002996
EST:     CTTGTTGCTGACTACATTGAAGTCATTAGCAAGCACAATGATGACAGCCA                         GTATGTATGGGAATCAAAGGCTGACGGTAAATTTGC
genomic: CTTGTTGCTGACTACATTGAAGTCATTAGCAAGCACAATGATGACAGCCAgtaagttgat ... ccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGC
EST: gi|164193803|gb|EL987107.1|EL987107
EST:     GAAGTCATTAGCAAGCACAATGATGACAGCCA                         GTATGTATGGGAATCAAAGGCTGACGGTAAATTTGCTGTTTCCGAGGATAC
genomic: GAAGTCATTAGCAAGCACAATGATGACAGCCAgtaagttgat ... ccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATAC
EST: gi|124728319|gb|EH819721.1|EH819721
EST:     CACAATGATGACAGCCA                         GTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATAC
genomic: CACAATGATGACAGCCAgtaagttgat ... ccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATAC
EST: gi|116483054|gb|EG525646.1|EG525646
EST:     CTTGTTGCTGACTACATTGAAGTCATTAGCAAGCACAATGATGACAGCCA                         GTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATAC
genomic: CTTGTTGCTGACTACATTGAAGTCATTAGCAAGCACAATGATGACAGCCAgtaagttgat ... ccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATAC
EST: gi|124892581|gb|EH971483.1|EH971483
EST:     CTTGTTGCTGACTACATTGAAGTCATTAGCAAGCACAATGATGACAGCCA                         GTATGTATGGGAATCAAAGGCTAACGGTAAAT
genomic: CTTGTTGCTGACTACATTGAAGTCATTAGCAAGCACAATGATGACAGCCAgtaagttgat ... ccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAAT
EST: gi|86067432|gb|DR363189.1|DR363189
EST:     CTTGTTGCTGACTACATTGAAGTCATTAGCAAGCACAATGATGACAGCCA                         GTATGTATGGGAATCAAAGGCTGACGGTAAATTTGCTGTTTCCGAGGATAC
genomic: CTTGTTGCTGACTACATTGAAGTCATTAGCAAGCACAATGATGACAGCCAgtaagttgat ... ccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgggcatgtaaaatcattgaaaagcttttctgataacttcttttccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATACATGGAATGAGCCTCTTGGACGTGGAACCGAGATTAGATTACATCTTAGG
                               tgataac  putative branch site (score: 2)
                                     cttcttttccgttttc  CT-rich tract
         taaaatcattgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgatttagagggctttgtttggcaatatacttgtgggcatgtaaaatcattgaaaagcttttctgataacttcttttccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATACATGGAATGAGCCTCTTGGACGTGGAACCGAGATTAGATTACATCTTAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA