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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtctgtcgtctgctagaccatcaggctactacggctgcttgagatctgtgtggtcatgctaaatttcatcattcagtagtttagtcgatgtctgaataaagatgtgttttctgtatgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAG

Basic information

species Zea mays
transcript GRMZM2G087192_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087192_T02 (Zea mays), 3'ss of exon 2
lower sequence: 13113.m00235 (Oryza sativa), 3'ss of exon 3
gtacgtctgtcgtctgctagaccatcaggctactacggctgcttgagatctgtgtggtcatgctaaatttcatcattcagtagtttagtcgatgtctgaataaagatgtgttttctgtatgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAG
    ||||||    | |||||   | |||||     | ||   ||| || |     | |||| | |||| | |  ||     ||| |  | || | | || |   |  ||||| ||||||||   |||||||||| || |||||||| ||||||||  | |||||||| ||||| |||||||| ||||||||||| |||||    |||||||| |||||||||||||||
----gtctgta---tcctagattgttaggctgt---gactttctgaaatttcatgagccatgttcaattgcct--tttgacggttcaa-caatctttaaagatcaa-atgtttcctgtatgcatgcaagGTACAAAGATACTCCTGGTATTTGGACAAAGGAGCAAGTGGAAGCGTGGAAGCCAATCGTAGACGGCGTTCATGCCAAAGGAGGAATATTTTTCTGTCAG

upper sequence: GRMZM2G087192_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ25413 (Selaginella moellendorffii), 3'ss of exon 2
gtacgtctgtcgtctgctagaccatcaggctactacggctgcttgagatctgtgtggtcatgctaaatttcatcattcagtagtttagtcgatgtctgaataaagatgtgttttctgtatgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAG
                                                   |||    | || |   ||||  |||||  | ||||    ||  |      ||   ||  |||    ||| |||| |               ||||| || ||| |  | |||||||||||||||||||||||||| ||  | |  |||||  | |||||||   | || ||    |||
---------------------------------------------------gtgaaagc-tgttc--tttctccattctcttgttttactgaact----gcaagcttggatttcagATATCCGCATAG-------------CCCTGGAATCTGGTCAGAGGAGCAAGTCGAAGCATGGAAGCCGATTGTCCAGGCTGTTCATGACAAAGGAGCTGTTTTCTTTCTACAG
















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|91878868|gb|EB408825.1|EB408825
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211459461|gb|FL315095.1|FL315095
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211046904|gb|FL342230.1|FL342230
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211434603|gb|FL306594.1|FL306594
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211538244|gb|FL353979.1|FL353979
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211438615|gb|FL361924.1|FL361924
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|78105288|gb|DV523706.1|DV523706
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCAT
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCAT
EST: gi|71766717|gb|DR964654.1|DR964654
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211372990|gb|FL342986.1|FL342986
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|78110280|gb|DV528695.1|DV528695
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|71769744|gb|DR967681.1|DR967681
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211004021|gb|FL317949.1|FL317949
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211049230|gb|FL320166.1|FL320166
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|71448418|gb|DR829468.1|DR829468
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|31363471|gb|CD447828.1|CD447828
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211516970|gb|FL321888.1|FL321888
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCAT
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCAT
EST: gi|211086396|gb|FL335516.1|FL335516
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|76017395|gb|DT944565.1|DT944565
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|71431905|gb|DR812955.1|DR812955
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211215728|gb|FL322479.1|FL322479
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211399636|gb|FL347340.1|FL347340
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACC-ATGAGCAAGTCGAAGCATGG
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGG
EST: gi|76281886|gb|DV021454.1|DV021454
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA

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: 49 (upstream exon), 44 (downstream exon)
Score: 50

ATGTTCCTCAGCCTCATGCCATACTGTACTATCAGCAGAGGGCGACTAAAGGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2872

ATGTTCCTCAGCCTCATGCCATACTGTACTATCAGCAGAGGGCGACTAAAGGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2517

ATGTTCCTCAGCCTCATGCCATACTGTACTATCAGCAGAGGGCGACTAAAGGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 588

ATGTTCCTCAGCCTCATGCCATACTGTACTATCAGCAGAGGGCGACTAAAGGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcagtagtttagtcgatgtctgaataaagatgtgttttctgtatgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAG
                        aataaagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtctgtcgtctgctagaccatcaggctactacggctgcttgagatctgtgtggtcatgctaaatttcatcattcagtagtttagtcgatgtctgaataaagatgtgttttctgtatgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG