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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCATGAGAGCCTGCAAAGGATACGTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatcctttctttttgtaaccattcaggtctttgttcgattgtctggcattaaaatttgtaagcatttcaactgcaacag

Basic information

species Zea mays
transcript GRMZM2G085970_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085970_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g06450.2 (Oryza sativa), 5'ss of exon 7
GTTCATGAGAGCCTGCAAAGGATACGTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatcctttctttttgtaaccattcaggtctttgttcga--ttgtctggcattaaaatttgtaagcatttcaactgcaacag
|| ||||||||||| |||||||||||||||||||||||||||||||| || || |||| |||||||||||||||||| ||        | |  ||| |      | || | |  |   | | || |||    |||| |    ||||||||||| ||||
GTCCATGAGAGCCTACAAAGGATACGTGAAAGGAAGCTTGTTAACTTCATTGAGTGGGGACCTGCAAGCATTCAGgtcat--------tatacaactagaataattttaggttaaacctttttgacatattgatttattgttatttcaactgccacag

upper sequence: GRMZM2G085970_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA03G41670.2 (Glycine max), 5'ss of exon 7
GTTCATGAGAGCCTGCAAAGGATACGTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatcctttctttttgtaaccattcag---gtctttgttcgattg--tctggcattaaa----atttgtaagcatttcaactgcaacag---
|||||||| ||  |||| ||||| |||||||| || || ||||||||||| || ||||  |||||||| ||||||||   | ||   | | ||| |   | |    ||||   ||  |||   | | | | | ||    || | |   | || | ||       |   
GTTCATGAAAGTTTGCAGAGGATTCGTGAAAGAAAACTGGTTAACTTTATTGAGTGGGGTCCTGCAAGTATTCAGgtctgcgttc--tgtggtagctggtgaatttgtctcctttgtattagttttaggactcaatctgatctttcttctttcctacacttctggtag

upper sequence: GRMZM2G085970_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA19G44260.2 (Glycine max), 5'ss of exon 8
GTTCATGAGAGCCTGCAAAGGATACGTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatcctttctttttgtaaccattcaggtctttgttcgattgtctggcattaaaatttgtaagcatttcaactgcaacag------------------
|||||||| ||  |||| ||||| |||||||| || || ||||||||||| || ||||  |||||||| ||||||||   | ||   |     ||| | | |           | |    | |   |    | | | ||  ||   |||  | | |                  
GTTCATGAAAGTTTGCAGAGGATTCGTGAAAGAAAACTAGTTAACTTTATTGAGTGGGGTCCTGCAAGTATTCAGgtctgcattctgtggcaaaacaaattaaagtggcagctggtgaatttgt-ctcctttatattagttttaggactcaatctgatctttcttctttcctag

upper sequence: GRMZM2G085970_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT3G61650.1 (Arabidopsis thaliana), 5'ss of exon 6
GTTCATGAGAGCCTGCAAAGGATACGTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatcctttctttttgt-----aaccattca--ggtctttgttcgattgt---ctggcattaaaatttgtaa-gcatttcaactgcaacag
|| ||||||||  |||| |||||||| ||||| ||||||||||| || || || |||| |||||||||||| |||||| |    |  || |||     ||  | | |  | | || | |  |   |   || | || | ||||| |     || | |    ||||||
GTGCATGAGAGTTTGCAGAGGATACGAGAAAGAAAGCTTGTTAATTTCATTGAGTGGGGACCTGCAAGCATACAGgttctaacctaattgtgtctgcaaattagttattgcttttggcttcaccatggacttgaatcataattttttccatatcttactctcaacag

upper sequence: GRMZM2G085970_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv15s0046g01350.t01 (Vitis vinifera), 5'ss of exon 7
GTTCATGAGAGCCTGCAAAGGATACGTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatcctttctttttgtaac---cattcaggtcttt------gttcgattgtctggcattaaaatttgtaagcatt-tcaactgcaacag--------------
|||||||| ||  |||| || ||||||||||| ||||||||||| ||||| || |||| ||||||||||||||||||| | ||   |  |   | |    ||| |  || ||       |||   | |||   ||||      |||| |||| ||   ||  |                 
GTTCATGAAAGTTTGCAGAGAATACGTGAAAGAAAGCTTGTTAATTTTATTGAATGGGGACCTGCAAGCATTCAGgtttttctccatgctaaaagcatttatttatatcattcagtccattcttctatctactattatgtggagtaaacattatcttttgtgatttctgttcttttgcag

upper sequence: GRMZM2G085970_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S266_15V6.1 (Physcomitrella patens), 5'ss of exon 7
GTTCATGAGAGCCTGCAAAGGATACGTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgtt---atcctt----tctttttgtaaccattcaggtctttgttcgattg---tctggcattaaaatttgtaagcatttcaactgcaacag---------
|||||  | || || ||||| ||||| ||||| ||||| | |||||| || || |||| ||||||||||||||||||    |  |||    | | ||        || | || |       ||||   |      || |||    || |||  ||   || |  |          
GTTCACAAAAGTCTACAAAGAATACGAGAAAGAAAGCTAGCTAACTTCATTGAATGGGGACCTGCAAGCATTCAGgtgtggaaacttaaagtttcttccatgtgttttatgtatcaacctcattgcaattctttgttgaaaaaactatgcagctcttttgaagtaaatatttggg

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|211101013|gb|FL440822.1|FL440822
EST:     GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAG                         GTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
EST: gi|60355250|gb|DN222223.1|DN222223
EST:     GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAG                         GTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGGGT
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGGGT
EST: gi|50330999|gb|CO526125.1|CO526125
EST:     GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAG                         GTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
EST: gi|60394883|gb|DN227752.1|DN227752
EST:     GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCCAGCCTTCAG                         GTTGCCCTGTCAAGA
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGA
EST: gi|37389993|gb|CF632221.1|CF632221
EST:     GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAG                         GTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
EST: gi|22819393|gb|BU499483.1|BU499483
EST:     GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAG                         GTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
EST: gi|12971802|gb|BG267665.1|BG267665
EST:     GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAG                         GTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
EST: gi|32933127|gb|CF037939.1|CF037939
EST:     GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAG                         GTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
EST: gi|211132309|gb|FL429622.1|FL429622
EST:     GTGAAAGGWAGCTTGTTAACTTTATAGACTGGGCAC-TGCAAGCATTCAG                         GTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
EST: gi|211056566|gb|FL481088.1|FL481088
EST:     GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAG                         GTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
EST: gi|93014105|gb|EB639625.1|EB639625
EST:     GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAG                         GTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
EST: gi|4647086|gb|AI622161.1|AI622161
EST:     GTGAAAGNAAGCTTGTTANCTTTATAGACTGGGCACCTGCAAGCATTCAG                         GTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
EST: gi|22542648|gb|BU093086.1|BU093086
EST:     GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAG                         GTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
EST: gi|76020288|gb|DT947458.1|DT947458
EST:     GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAG                         GTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
EST: gi|22935439|gb|BU571714.1|BU571714
EST:     GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAG                         GTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
EST: gi|83278659|gb|DV942667.1|DV942667
EST:     GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAG                         GTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG
genomic: GTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG

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), 43 (downstream exon)
Score: 56

GTTCATGAGAGCCTGCAAAGGATACGTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG


Block sizes: 38 (upstream exon), 22 (downstream exon)
Score: 12

GTTCATGAGAGCCTGCAAAGGATACGTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 17

GTTCATGAGAGCCTGCAAAGGATACGTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 47

GTTCATGAGAGCCTGCAAAGGATACGTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatccttt ... actgcaacagGTTGCCCTGTCAAGAAAATCCCCATATGTTCAAACAACCCACAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCATGAGAGCCTGCAAAGGATACGTGAAAGGAAGCTTGTTAACTTTATAGACTGGGCACCTGCAAGCATTCAGgttatcctttctttttgtaaccattcaggtctttgttcgattgtctggcattaaaatttgtaagcatttcaactgcaacag

- - - - - - - - - - - - - -  AAGGAA