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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgcattgtgctaatattgtagcaattagcaaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC

Basic information

species Zea mays
transcript GRMZM2G136069_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G08610.1 (Glycine max), 3'ss of exon 6
gtattgcattgtgctaatattgtagcaattagcaaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC
|| |||||      || ||| |||     ||     |||    |||  |          |  | |    |   | |   |   |||  ||   |    || | | |||||||||||||||||||| ||  ||||| ||| ||| ||||||||||||||||||||||  || |     ||||| || |  || ||||||| ||| ||  
gtcttgcaagactatagtatagtatgtggtactggtctaaggttatcaat--------aaatattaatccacatttcaataacaacatttctgacctgtatactacagATGGCAGATCCTTTGACGGCTTTGATGCATGTAGTACAAGTGATGAATTTTCTCAAGACCCTTGAGATGAAGACACTAAGAGAAAGAGAGGGGTCTACGG

upper sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G09560.1 (Glycine max), 3'ss of exon 5
gtattgcattgtgctaatattgtagcaattagcaaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC
||      || ||   |||    || | | |  |  | |     ||| |  | | |   | |    |   ||||     | |  | | ||||     ||    ||||||||||||| |||||||||||| ||||||||||||| ||||||||||| || || ||||  ||  ||  || ||||||    || ||| || | |      
gtgccat-ttttgtccata---gagtagtgaagatgccaatgtgatacagttgatct--atcttatggttggtttcagttacagaat-ttagtctttttg-gttgcagATGGCAGACCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTGAAGAATCTTATATTAAGGACCCTGCGAGAAAGAAAGTATTGTGTCG

upper sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G38120.1 (Glycine max), 3'ss of exon 4
gtattgcattgtgctaatattgtagcaattagcaaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC
      | |  | ||| |||  ||   |  |    | |     | | |   |       | |  |||     | |   |   |   |  | |||    |    | |||||||||||||||||||||||  ||||||||||||| ||||| ||||||||||||||||  || ||    ||| |  | |  || |||||||| || | | 
-----tcttgtttctagtatgttacacaaaattctagtgctggtctgtggttatgattaatctatggtgaaataaca-gcatttctttctggcatgtcttt--tacagATGGCAGATCCTTTGACTGCTTTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTTGTGAAGGCATTGAGAGAAAGAGAGGAATCTATTG

upper sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G18900.1 (Glycine max), 3'ss of exon 6
gtattgcattgtgctaatattgtagcaattagcaaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC
||      || ||   |||    || | | |  |  | |     |||||  | | |        ||| | ||||     | |  | | ||||      |    |||||||||||||||||||||||||| ||||||||||||| ||||||||||| || || ||||  ||  ||  || ||| ||    || ||| |||| |      
gtgccat-ttttgtccata---gagtagtgaagatgccaatgtgatatagttgatct-atcttatggta-ggtttcagttacagaat-ttagtctttctg-gttgcagATGGCAGATCCTTTGACTGCATTGATGTATGCAGTTCAAGTGATGAACTTCCTAAAGAATCTTATATTAAGGACACTGCGAGAGAGAAAGGATTGTGTGG

upper sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G35480.1 (Glycine max), 3'ss of exon 4
gtat-tgca--ttgtgctaatattgtagcaattagcaaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC
|| | ||||  ||    |||| ||||  | | | ||      |   | |||   | | |       ||| ||   |||     || |    ||  ||    |    | ||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||||||||  || ||    ||||| || |  || |||||||| || | | 
gtgtgtgcaagttcctttaatcttgtttctagt-gctgttctgtggt-tatgattaatct---atggtgaaa---ttaca---gcaattctttctcacgtgtctcctacagATGGCAGATCCTTTGACTGCTCTGATGTATGCAGTACAAGTCATGAATTTTCTCAAGACTCTTGTGGTGAAGACACTGAGAGAAAGAGAGGAATCTATTG

upper sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G08340.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------------------gtattgcattgtgctaatattgtagcaattagcaaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttaca-atgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC
                                                                              ||   ||  ||    | |    |      ||  || |||||    ||   ||  |   | |   |||    | |   ||  |  || |        ||     || |||||||||| ||||| |||||| |||||||||| |||||||||||||| || |||||||  ||   | | |||||  | |  || || || |  ||| || 
gtcagtctttttttattaccaacactaaaatgcacaagttacactctcattaagcatgtgtttgattaatggctgcaataaatcaccgtatagagagctaatatgacagttaaatagcagagcatgattctac---aacttcggaggtttgaaatgtattggctctgttttggtttttgtgtgtagATGGCAGACCCTTTAACTGCATTGATGTATGCGGTCCAAGTGATGAAGTTGCTCAAGAGCCTCACAGAGAAGACTGTGAGAGAAAGGGAAGCTTCCTCTT

upper sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT5G22400.1 (Arabidopsis thaliana), 3'ss of exon 4
gtattgcattgtgctaatattgtagcaattag-caaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC
              | |   || | |||  ||    | || |||| | || |||      ||   ||| |     |||  ||  ||        | ||||  | || ||||||  |||||  |||| |||||||||||||| || ||||||||||| ||||||||||  ||  |  |||| ||  | |  || ||  | || ||     
-------------gtgagtctgcaacaacaaggttgattatcaatgtttaactcggggtcag--atgggataaa-atgattgagaa--------acacttgtattgtagATGGATGATCCACTGACAGCACTGATGTATGCGGTTCAAGTGATGAACTTTCTCAAGACACTAATCGAAAAAACTTTAAGAGAAAGGCAAGACTCAGTGG

upper sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0080g00580.t01 (Vitis vinifera), 3'ss of exon 4
gtattgcattgtgctaatattgtagcaattagcaaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaactta---caatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC
     |||||    ||| |||    |||| |  ||  || || | |||   ||  |    |       |     ||  ||   | |  |        |     ||    |||||||||||||| |||||||| |||||||||| |||||||| |||||||| |||||||  ||  |   |||||| ||    || ||||| || || |   
-----gcatt---ttaagattt---caatcaataatttatcattttatcgttctgcaactgtttcaataacaccattggtaacagccttctatgttttcttctcatcatagATGGCAGATCCTCTGACTGCATTGATGTATGCTGTCCAAGTCATGAATTTCCTCAAGACACTTATCATAAAGACACTACGAGAAAGAGAAGATTCAATGG

upper sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0007g03140.t01 (Vitis vinifera), 3'ss of exon 4
gtattgcattgtgctaat--attgtagcaattagcaaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC
 |  |   ||     ||   | ||  |   ||   |   |   |   | |    ||  | |  || ||  | |   |    |     || || |           |||||||||||||||| ||||| ||  ||||||||||||||||||||||||||||||||||||   || ||   | ||| || | ||| || ||||| || |   
atcctcttttaaataaactcactgatgtttttcttattttgatatagttttgtacattctggtcaatgtgaggtgcaatgatatcttctgttggt----------tgcagATGGCAGATCCCTTGACAGCCTTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGACTTTGATAATCAGGACGCTTAGGGAAAGGGAGGACTCAATAG

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: 55

CTAGGCTGTTAATCTGATGGATGATGTAGTCCAGGAAGAACAGATAAACAAGATGAATGATCACAATATTGCTATGGTTTTTGTGCCAAATACGACTCAGgtattgcatt ... tacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 32

CTAGGCTGTTAATCTGATGGATGATGTAGTCCAGGAAGAACAGATAAACAAGATGAATGATCACAATATTGCTATGGTTTTTGTGCCAAATACGACTCAGgtattgcatt ... tacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 28

CTAGGCTGTTAATCTGATGGATGATGTAGTCCAGGAAGAACAGATAAACAAGATGAATGATCACAATATTGCTATGGTTTTTGTGCCAAATACGACTCAGgtattgcatt ... tacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 25

CTAGGCTGTTAATCTGATGGATGATGTAGTCCAGGAAGAACAGATAAACAAGATGAATGATCACAATATTGCTATGGTTTTTGTGCCAAATACGACTCAGgtattgcatt ... tacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC
                             taactatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgcattgtgctaatattgtagcaattagcaaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG