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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtatagaggttttgttatgtcacagtaatatatgtagattacattgcatgtttatttgcaaagtctagtatttttaacctatgttttgggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAGAGCAAGACTTACATGGAGGTAAAGGGTACCGGTACGGCAAACCAGTGTC

Basic information

species Arabidopsis thaliana
transcript AT3G50820.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G50820.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g31690.1 (Oryza sativa), 3'ss of exon 1
---------------gtgtatagaggt-tttgttatgtcacagtaatatatgtagattacattgcatgtttatttgcaaagtctagtatttttaacctatgtt--ttgggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAGAGCAAGACTTACATGGAGGTAAAGGGTACCGGTACGGCAAACCAGTGTC
               |  | |||  || | |   ||| | |  |     | |   |        |   |  | || | |  | |   |       | | || |    ||    || |||| ||| | |||||||| |  || | |||||| || | ||||||||| ||||| ||||| ||||||||||| ||||| ||||| ||||| |||||||| |
gtaagaccttaattaggatttaggagtatgttgcatggcgccatggccaaggccaaggtggaaacg-atcgaattactatatatgtaacgccgtgcatgtggtggccggccggtgtagGGCGCCAGCGCGGAGGGCGTGCCGAGGAGGCTTACCTTCGACGAGATTCAGAGTAAGACGTACATGGAGGTGAAGGGAACCGGCACGGCGAACCAGTGCC

upper sequence: AT3G50820.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G113349_T01 (Zea mays), 3'ss of exon 1
gtgtatagaggttttgttatgtcacagtaatatatgta-gattacat-tgcatgtttatttgcaaagtctagtatttttaacctatgttttgggta-atgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAGAGCAAGACTTACATGGAGGTAAAGGGTACCGGTACGGCAAACCAGTGTC
||   || | | |  |   ||    |  |  |    || | |||| | ||| || |  |   ||| ||| |    |   | |  |||    | ||    | |||| ||  | ||||||||  | || |||||||| || ||||||||||| ||||||||||| ||| ||||||| ||||| || || ||||| |||||||| |
gtaagtataagataagc-gtgcattatcagcaagcttacgcttacctgtgcctgctcctcaacaacgtcga----tcgaagctgatgacacgtgtgtgcgcagGGCGCGAGCGCGGAGGGCACGCCCAAGAGGCTGACCTACGACGAGATCCAGAGCAAGACGTACCTGGAGGTGAAGGGCACGGGCACGGCGAACCAGTGCC

upper sequence: AT3G50820.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G175562_T02 (Zea mays), 3'ss of exon 1
---------------------------gtgtatagaggttttgttatgtca--cagtaatatatgtagattacat-tgcatgtttatttgcaaagtctagtatttttaacctatgttttgggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAGAGCAAGACTTACATGGAGGTAAAGGGTACCGGTACGGCAAACCAGTGTC
                             |  |    | |     | |||   |     |   ||  | | |||| ||  ||| | | ||         || | | |    | ||| |       || |||| ||  | ||||||||  | || |||||||| || ||||||||||| |||||||| || ||||||||||| ||||| || || ||||| |||||||| |
gtaagcacgcatgcattgttagcgagctcgcttgcctgctcctcaaggtcggccgaagttggttggtggtgacatgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg-tgtgtgtgtgtctgcgtgcagGGCGCGAGCGCGGAGGGCACGCCCAAGAGGCTGACCTACGACGAGATCCAGAGCAAAACGTACATGGAGGTGAAGGGCACGGGCACGGCGAACCAGTGCC

upper sequence: AT3G50820.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G25860.1 (Glycine max), 3'ss of exon 1
gtgtatagaggttttgttatgtc-acagtaatatatgtagattacat-tgcatgtttatttgcaaagtctagtatttttaaccta-tgttttgggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAGAGCAAGACTTACATGGAGGTAAAGGGTACCGGTACGGCAAACCAGTGTC
      | |         |   | |    | | ||| ||  ||   |   ||  |||| || | |     | | |   | ||  | ||     ||  ||  |||||||  |||| || || |  |||||||||||||| | |||||| || ||||||||||| ||| |||| || ||||| || || || ||||||||||| |
---agaaaacacccaaaaacacctattaaagtgtatctaagttttgtactcacttttaattactattggcattgtacatgactaactgagcaaggacatatagGGGGCAAGTGCTGAAGGTGTTCCAAAGAGGCTAACCTTCGACGAAATCCAGAGCAAGACCTACTTGGAAGTGAAGGGGACAGGAACAGCAAACCAGTGCC

upper sequence: AT3G50820.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G06830.1 (Glycine max), 3'ss of exon 1
gtgtatagaggttttgttatgtcacagtaatatatgta-gattacattgcatgtttatttgcaaagtctagtatttttaacctatgttttgggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAGAGCAAGACTTACATGGAGGTAAAGGGTACCGGTACGGCAAACCAGTGTC
   | |  | | |||   |        |  ||     | || |   | | || | | ||    |    | | | | |  |   |||  |  |  |||  |||||||  |||| || |||| ||||||| ||||||| |  ||||| || ||||||||||| ||| |||| || ||||| || || || |||||||||||||
-attttgaaagctttagaaaaaggtgttgttaacaacatgagtgagtggtatttctgttcattactattggcaatgtacatgaatgactaagaaaattcagGGGGCAAGTGCTGAAGGAGTACCAAAGCGGCTAACCTTTGACGAAATCCAGAGCAAGACCTACTTGGAAGTGAAGGGGACAGGAACAGCAAACCAGTGTC

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|124764659|gb|EH854789.1|EH854789
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCA
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCA
EST: gi|125300533|gb|EL314618.1|EL314618
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAG
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAG
EST: gi|124874110|gb|EH955755.1|EH955755
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGA
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGA
EST: gi|125042868|gb|EL115137.1|EL115137
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGAT
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGAT
EST: gi|124863071|gb|EH947508.1|EH947508
EST:     TCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAG
genomic: TCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAG
EST: gi|125244156|gb|EL258241.1|EL258241
EST:     CCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAG
genomic: CCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAG
EST: gi|124813565|gb|EH898431.1|EH898431
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCACCAAAGAAGGCTAACGTACGACGAGATACA
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGA-GGCTAACGTACGACGAGATACA
EST: gi|124757081|gb|EH847211.1|EH847211
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGA
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGA
EST: gi|125231766|gb|EL245851.1|EL245851
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATAC
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATAC
EST: gi|47831580|gb|CK121264.1|CK121264
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAG
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAG
EST: gi|125299543|gb|EL313628.1|EL313628
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGC
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGC
EST: gi|124910229|gb|EH984309.1|EH984309
EST:     CCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAG
genomic: CCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAG
EST: gi|124827455|gb|EH912321.1|EH912321
EST:     TCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGNGATACA
genomic: TCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGG-TGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACA
EST: gi|125265456|gb|EL279541.1|EL279541
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCATTGTCTCG                         GGGGCCGGTGCGGA
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGA
EST: gi|125020121|gb|EL092390.1|EL092390
EST:     TCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTA
genomic: TCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTA
EST: gi|116459735|gb|EG502327.1|EG502327
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCA
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCA
EST: gi|125295977|gb|EL310062.1|EL310062
EST:     CGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGACTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAG
genomic: CGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTG-CTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAG
EST: gi|116459732|gb|EG502324.1|EG502324
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCA
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCA
EST: gi|124909395|gb|EH983475.1|EH983475
EST:     CCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGAATACA
genomic: CCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGA-TACA
EST: gi|125134460|gb|EL175364.1|EL175364
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAG
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAG
EST: gi|116458437|gb|EG501029.1|EG501029
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGC
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGC
EST: gi|124913246|gb|EH987120.1|EH987120
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCACCAAA
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAA
EST: gi|124718805|gb|EH810207.1|EH810207
EST:     CCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAG
genomic: CCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAG
EST: gi|125289574|gb|EL303659.1|EL303659
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGACGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACA
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTG-CGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACA
EST: gi|116458438|gb|EG501030.1|EG501030
EST:     CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCG                         GGGGCCGGTGC
genomic: CCGCCAAGATCGCCGGTTTTGCTCTAGCCACCTCTGCTCTCGTTGTCTCGgtataacttc ... ggtaatgaagGGGGCCGGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatgtttatttgcaaagtctagtatttttaacctatgttttgggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAGAGCAAGACTTACATGGAGGTAAAGGGTACCGGTACGGCAAACCAGTGTC
                            ttttaac  putative branch site (score: 2)
                    tctagtatttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtatagaggttttgttatgtcacagtaatatatgtagattacattgcatgtttatttgcaaagtctagtatttttaacctatgttttgggtaatgaagGGGGCCGGTGCGGAGGGAGCACCAAAGAGGCTAACGTACGACGAGATACAGAGCAAGACTTACATGGAGGTAAAGGGTACCGGTACGGCAAACCAGTGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - -ggttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaagtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg