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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTGCACTTTCAACCTTGACATAATTTCTGTGAAGAAAAACCCAAATGGTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaagcatttttaccagttattgtagtcaatacttttgtgtagtgactgtattaggtgctagccatggttcactgagattacctctttatatcaccccctcccctcccctctatcgaaattgctgctcacaatagtattctttcag

Basic information

species Zea mays
transcript GRMZM2G174204_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174204_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 5'ss of exon 7
GAAGTGCACTTTCAACCTTGACATAATTTCTGTGAAGAAAAACCCAAATGGTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaagcatttttaccagttattgtagtcaa--tacttttgtgtag--tgactgtattaggtgctagccatggttcactga-gattacctctttatatcaccccctcccctcccctctatcgaaattgctgctcacaatagtattctttcag
||| || ||||||||||||||||||||||||||||||||||||||||||||||  |||||| || ||||||||||| ||||||||||||| ||||||||||||   |||| ||| |  |    |||   |   ||  || | |  | ||   ||   ||||||   |||     ||  | | |||  || |   |||||                                                         
GAAATGTACTTTCAACCTTGACATAATTTCTGTGAAGAAAAACCCAAATGGTCAAATGTACTCTACTCTTGGTGTTTTGACAAGGGGAACTATCATTGAGgtatgtcaagaattctgcctgtatatgaaaacaaaagtaatctcatttaagttgttagtattaca-gctgatagtgaattattgataatgaaaactttagc-------------------------------------------------------

upper sequence: GRMZM2G174204_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA02G35500.2 (Glycine max), 5'ss of exon 7
GAAGTGCACTTTCAACCTTGACATAATTTCTGTGAAGAAAAACCCAAATGGTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaagcatttttaccagttattgtagtcaatacttttgtgtagtgactgtattaggtgctagccatggttcactgagattacctctt-tatatcaccccctcccctcccctc--tatcgaaat-----tgctgctcacaatagtattctttcag
 || ||||| ||||| || ||  |||||   |||||||||||||| ||||| || |||||||| ||||||||||| || || | |||||| || ||||||||| |      ||||   |      || || |  |   || | |  | |  |  | | |||   |     || ||| |  |  || ||  || ||||      |   |       ||  |||| ||||     |  | ||    ||| |    ||||||
TAAATGCACATTCAATCTAGAATTAATTGGAGTGAAGAAAAACCCCAATGGCCCTATGTACACCTCTCTTGGTGTCATTACCAAGGGAACTATAATTGAGgtatttatgttatttcctc------ttctaattgagggttatttccactctcaatttaaggcatt---tctgcttctcctaacttgccctttctataatgtagctgtcgtatgaatcattatcaaaatgtacttatttctttgcatactgcaatttcag

upper sequence: GRMZM2G174204_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA10G00490.1 (Glycine max), 5'ss of exon 7
GAAGTGCACTTTCAACCTTGACATAATTTCTGTGAAGAAAAACCCAAATGGTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaagcatttttaccagtta-ttgtagtcaatactt--ttgtgtagtgactgtattaggtgctagccatggttcactgagattacctctttatatcaccccctcccctcccctctatcgaaattgctgc-tcacaatagtattctttcag------------------------
 || ||||| ||||| || ||  |||||   |||||||||||||| ||||| || |||||||| ||||||||||| || || |||||||| || ||||||||| |       |||   |   | | || || |  ||  ||  ||    | | ||  |   |||   | |   || | |  | |  |  ||||| ||| |       | | ||    | ||  | |  ||     | |  | | | |  |                             
TAAATGCACATTCAATCTAGAATTAATTGGAGTGAAGAAAAACCCCAATGGCCCTATGTACACCTCTCTTGGTGTCATTACCAGGGGAACTATAATTGAGgtatttatgctgtttcctcttctaaattctaattgatggttatttccacactcacaattgaaggcatttgagttgatcc--taacttgccctctctatttgctgatatgcactgatgtataatgtagctgtaatattatcaaaatgtgttgcttatttctttgcatactgcaatttcag

upper sequence: GRMZM2G174204_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA10G10000.1 (Glycine max), 5'ss of exon 7
GAAGTGCACTTTCAACCTTGACATAATTTCTGTGAAGAAAAACCCAAATGGTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaagcatttttaccagtta-ttgtagtcaatacttttgtgtagtg--actgtattaggtgct--agccatggttcactgagattacctctttatatcaccccctcccctcccctctatcgaaattgctgctcacaatagtattctttcag----------------------
 || ||||| ||||| || ||  |||||   |||||||||||||| ||||| || |||||||| ||||||||||| || || |||||||| || ||||||||| | |     |||   |   | | || || |  ||  || | |  | |   ||  | | |||   |  ||      | ||||||  |    | ||  |   |  | ||    |          | |||   |  ||| ||  || ||  ||                         
TAAATGCACATTCAATCTAGAATTAATTGGAGTGAAGAAAAACCCCAATGGCCCCATGTACACCTCTCTTGGTGTCATTACCAGGGGAACTATAATTGAGgtatttctgctgtttactcttctaaattctaattgatggttatttccactctcacaatttaaggcatttgagttgatatgcactgatttataatgttgctgatatgcactgatgtatatgtagctgtaat--attatcaaaaatgtgttgcttatttctttgcatactgcaatttcag

upper sequence: GRMZM2G174204_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 5'ss of exon 7
GAAGTGCACTTTCAACCTTGACATAATTTCTGTGAAGAAAAACCCAAATGGTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaagcatttttaccagttattgtagtcaatacttttgtgtagtgactgtattaggtgctagccatggttcactgagattacctctttatatcaccccctcccctcccctctatcgaaattgctgctcacaatagtattctttcag
 || ||||||||||||||||| ||||||   || |||||||| || ||||| |  ||||| ||||| |||||||||||||| | ||| || |||||||||||| |   |    || |      | || ||          |  |||  | | |  || |     |  | |   | || || |||   ||||||||  |     ||||  |      ||                                 
CAAATGCACTTTCAACCTTGAGATAATTGGAGTAAAGAAAAATCCTAATGGCCAAATGTATACTTCCCTTGGTGTTATGACCAAGGGTACTATCATTGAGgtaat---atttcttcttttgactcttata----------tgatgtgataaattgatgacaaatttactac--tccaatgtgatggtctctttattgctgatgctcctgttaatggtag--------------------------------

upper sequence: GRMZM2G174204_T01 (Zea mays), 5'ss of exon 7
lower sequence: EFJ15002 (Selaginella moellendorffii), 5'ss of exon 7
GAAGTGCACTTTCAACCTTGACATAATTTCTGTGAAGAAAAACCCAAATGGTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaagcatttttaccagttattgtagtcaatacttttgtgtagtgactgtattaggtgctagccatggttcactgagattacctctttatatcaccccctcccctcccctctatcgaaattgctgctcacaatagtattctttcag
 ||||| || ||| | ||||| ||  ||  ||||||||||||||| || || || |||||||| || || ||||| || || |||||||| ||||| ||||||     ||     ||    | | ||||   | |  ||||| | ||      | | |   | | ||                                                                                    
CAAGTGTACATTCCAGCTTGAAATCCTTGGTGTGAAGAAAAACCCGAACGGCCCCATGTACACGTCCCTGGGTGTGATAACTAGGGGAACGATCATCGAGgta-----ag-----ttgatgggttttgtttcctaagcttttttatatcattcgaaatgttttccag------------------------------------------------------------------------------------

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|17931305|gb|BM268265.1|BM268265
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|37398604|gb|CF636617.1|CF636617
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|45847995|gb|CN071938.1|CN071938
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTTTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|71440545|gb|DR821595.1|DR821595
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|60347312|gb|DN214285.1|DN214285
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|76917032|gb|DV166647.1|DV166647
EST:     TCCGAGGTACACTTCTCTGGGTGTTATGACAAGGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: TCCGATGTACACTTCTCTTGGTGTTATGACAA-GGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|50332540|gb|CO527666.1|CO527666
EST:     GTCCGATGTACACTTTTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTTTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|211296298|gb|FL480002.1|FL480002
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|45847152|gb|CN071095.1|CN071095
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|211523708|gb|FL481391.1|FL481391
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|60354693|gb|DN221666.1|DN221666
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|78109119|gb|DV527536.1|DV527536
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|71440546|gb|DR821596.1|DR821596
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|5739867|gb|AI947557.1|AI947557
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|17930472|gb|BM267432.1|BM267432
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|45847376|gb|CN071319.1|CN071319
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|60350420|gb|DN217393.1|DN217393
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|211487760|gb|FL392997.1|FL392997
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|60340980|gb|DN207953.1|DN207953
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|37386665|gb|CF630520.1|CF630520
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
EST: gi|24766881|gb|CA402026.1|CA402026
EST:     GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGACCAATCATTGAG                         GTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG
genomic: GTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGG

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), 49 (downstream exon)
Score: 174

GAAGTGCACTTTCAACCTTGACATAATTTCTGTGAAGAAAAACCCAAATGGTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 138

GAAGTGCACTTTCAACCTTGACATAATTTCTGTGAAGAAAAACCCAAATGGTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 113

GAAGTGCACTTTCAACCTTGACATAATTTCTGTGAAGAAAAACCCAAATGGTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 56

GAAGTGCACTTTCAACCTTGACATAATTTCTGTGAAGAAAAACCCAAATGGTCCGATGTACACTTCTCTTGGTGTTATGACAAGGGGAACAATCATTGAGgtactccaag ... attctttcagGTAAATGTCAGTGAGCTTGGTCTGGTAACTCCCGCTGGAAAAGTTGTTTGGG