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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgtttatagtttgtaaattgtaagtgatgctactatgagaacttggttcatttaatgatatttatatttctcaaattttgtttgtttctttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG

Basic information

species Zea mays
transcript GRMZM2G057408_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057408_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g45840.2 (Oryza sativa), 3'ss of exon 1
attgtttatagtttgtaaattgtaagtgatgctactatgagaacttggttcattta-atgatatttatatttctcaaat------tttgtttgtttctttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG
      | |  |   |||| | |   || || |   ||   || | || |  |  |  |  | |  | |  ||| ||||        | ||  ||| |||| | ||| || |||||||||||||| || ||||||||||| ||||||||||| ||||| ||||||
------tttgatcgctaaaattttcttgttgat-taattgtaattagggtggtcaatgttgtgtacacacctcttaaatgtgcttccttttcttttgtttgatttagGTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAG

upper sequence: GRMZM2G057408_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G29740.1 (Glycine max), 3'ss of exon 1
attgtttatagtttgtaaattgtaagtgatgctactatgagaacttggttcatttaatgatatttatat-------ttctcaaattttgtttgtttctttgttgt----agTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG
          ||||  |||||  |  |  || |  | |     |||  || || |   | |    || |       | ||||  |||| |    ||| ||  |||    || ||||||||||||||||| || |||||||||| |||||| ||||||| ||||||||||
----------gttt-caaattaaagctagtgtttgtttctcccctttctttatcttggggtcgccatttgccactatcctcactttttttccccttcatttctgttttcagGTTTGATCGTGATTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGTTATACAG

upper sequence: GRMZM2G057408_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv16s0050g01180.t01 (Vitis vinifera), 3'ss of exon 1
----attgtttata-gtttgtaaattgtaagtgatgctactatgagaacttggttcatttaatgatatttatatttctcaaattttgtttgtttctttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG
    ||       | |  ||||  || | |||  |    ||       | |  || ||  | |  | |  |||  |     ||||||||  |   | |  |  |||||||| ||||||||||| || ||||| |||| |||||| |||||||| ||||| |||
aatcatcaccagaatgggtgtatcttttcagtt-tatctcttcttattcctaattaatggattagtttccataaatt---gattttgttattgattctact-cagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAG

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|71448760|gb|DR829810.1|DR829810
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|101392321|gb|EB818090.1|EB818090
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|211503271|gb|FL119712.1|FL119712
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|91876492|gb|EB406449.1|EB406449
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|211500941|gb|FL119710.1|FL119710
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|211503273|gb|FL119714.1|FL119714
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|50336085|gb|CO531211.1|CO531211
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTT-GATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|211503279|gb|FL119720.1|FL119720
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|211503277|gb|FL119718.1|FL119718
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|89755460|gb|DY685870.1|DY685870
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|78118283|gb|DV536669.1|DV536669
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|89757689|gb|DY687184.1|DY687184
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|78076508|gb|DV504942.1|DV504942
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|211503280|gb|FL119721.1|FL119721
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|211500936|gb|FL119705.1|FL119705
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|148963456|gb|EE014475.2|EE014475
EST:     AGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCACAGACTGT
genomic: AGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGG-CCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|148956892|gb|EC902815.2|EC902815
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|71441161|gb|DR822211.1|DR822211
EST:     GAGAGCTGGATGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|71428977|gb|DR810027.1|DR810027
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|211503278|gb|FL119719.1|FL119719
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|211500940|gb|FL119709.1|FL119709
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
EST: gi|211500939|gb|FL119708.1|FL119708
EST:     GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCT                         TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT
genomic: GAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 79

AGGAGGAGGTTCGGAAGGTCAGGAAGCCGTACACCATCACCAAGTCGCGGGAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

AGGAGGAGGTTCGGAAGGTCAGGAAGCCGTACACCATCACCAAGTCGCGGGAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 111

AGGAGGAGGTTCGGAAGGTCAGGAAGCCGTACACCATCACCAAGTCGCGGGAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

AGGAGGAGGTTCGGAAGGTCAGGAAGCCGTACACCATCACCAAGTCGCGGGAGAGCTGGACGGAGCCGGAGCACGACAAGTTCCTCGAGGCCCTGCAGCTgtgagtgccc ... tttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttcatttaatgatatttatatttctcaaattttgtttgtttctttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG
      atttaat  putative branch site (score: 92)
                                ttttgtttgtttcttt  putative PPT
      atttaatgatatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgtttatagtttgtaaattgtaagtgatgctactatgagaacttggttcatttaatgatatttatatttctcaaattttgtttgtttctttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC