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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgatttgcataatctgttttgtcgattcttgattcattataaattattttgctgatgcattcggcttctcttaacgatgccttgcactaaccacaaacatgtatgatgcatggcttaatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATGGGTGAAGCTAGACTGATAGATTCAGAGGACATGAGAGCAGCAGCATGGA

Basic information

species Zea mays
transcript GRMZM2G037926_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037926_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g33310.1 (Oryza sativa), 3'ss of exon 2
----------gtacgatttgcataatctgttttgtcgat-----tcttgattcattata--aattattttgctgatgca--ttcggcttctcttaacgatgccttg-cactaaccacaaacatgtatgatgcatggcttaatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATGGGTGAAGCTAGACTGATAGATTCAGAGGACATGAGAGCAGCAGCATGGA--
          |      |    || | ||||  ||  ||      || ||| |||| |   |||     ||    ||||  || |   |    ||| | ||  ||  | || ||    ||  |   |  |   || | ||||||||||||| |||||||||||||| |||||||||||||| || ||| ||||||||||||| ||||||||||||||||||   |||| | ||  |  ||| ||||||  
gtacgatcttgctttgctcttctattatgttcagtaaatatatccctggatgcattgtgataatgtccatggccttgcaacttagaaatactataatggtgtattatcgctgactgacaatttaact--tctttgtcgtaatcttcagGTATAACTTTGATCCTGTGAATGACTGCCCTCTTCCCGGCCGGTTTGAATGGGTCAAGCTAGACTGATAGATTTTCAGGAAAAGAAGG--GCACCATGGACC

upper sequence: GRMZM2G037926_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G32710.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacgatttgcataatctgttttgt-cgattcttgattcattataaattattttgctgatgcattcggcttctcttaacgatgccttgcactaaccacaaacatgtatgatgcatggcttaatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATGGGTGAAGCTAGACTGATAGATTCAGAGGACATGAGAGCAGCAGCATGGA-
||| |  || | |  | |  | ||| |  |||||  ||  |||| | ||       || |   |||  ||  | |       | ||||   |  |   ||   | | ||        ||   ||||||||||||||||||||||||| || ||    || || |||||  |||||||||||  |||| ||||    ||||  ||    | |   | |  |    || |  
gtatgtgtttcctcgtttcatctgttctgttctt--ttggttatgagtttccagtttgttctgttcttctcttttg------gtcttg---tgtctctaatggtttctgtc----aactctttcttcagGTACAACTTTGATCCTGTGAACGAACAACCACTACCAGGACGGTTTGAATGGACGAAGGTAGATGATTAGAAACAACAAAAAAATGGGGGGTTA-ATAGTT
















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|32801050|gb|CD953286.1|CD953286
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
EST: gi|9731261|gb|BE510013.1|BE510013
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
EST: gi|32803586|gb|CD955822.1|CD955822
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
EST: gi|211331095|gb|FL451168.1|FL451168
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAGGTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
EST: gi|32789091|gb|CD941327.1|CD941327
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
EST: gi|211236991|gb|FL432207.1|FL432207
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
EST: gi|110518064|gb|EE022651.1|EE022651
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
EST: gi|78080379|gb|DV508791.1|DV508791
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
EST: gi|32803413|gb|CD955649.1|CD955649
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
EST: gi|60350857|gb|DN217830.1|DN217830
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
EST: gi|32803731|gb|CD955967.1|CD955967
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
EST: gi|32804950|gb|CD957186.1|CD957186
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
EST: gi|6653965|gb|AW267370.1|AW267370
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
EST: gi|32825526|gb|CD965248.1|CD965248
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
EST: gi|78080378|gb|DV508790.1|DV508790
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
EST: gi|32800885|gb|CD953121.1|CD953121
EST:     GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAA                         GTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG
genomic: GAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATG

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: 109

GGGTGAAAGCTCCTCCTGTGCACGCCATCCCAAGTTCAACGGAGATGAACGAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATGGGTGAAGCTAGACTGATAGATTCAGAGGACATGAGAGCAGCAGCATGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 17

GGGTGAAAGCTCCTCCTGTGCACGCCATCCCAAGTTCAACGGAGATGAACGAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATGGGTGAAGCTAGACTGATAGATTCAGAGGACATGAGAGCAGCAGCATGGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 38

GGGTGAAAGCTCCTCCTGTGCACGCCATCCCAAGTTCAACGGAGATGAACGAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATGGGTGAAGCTAGACTGATAGATTCAGAGGACATGAGAGCAGCAGCATGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 43

GGGTGAAAGCTCCTCCTGTGCACGCCATCCCAAGTTCAACGGAGATGAACGAGTACTTCGCTGCTGAACAGCGACGCCAACAACAGGCTTTCATTGACAAgtacgatttg ... taatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATGGGTGAAGCTAGACTGATAGATTCAGAGGACATGAGAGCAGCAGCATGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaacgatgccttgcactaaccacaaacatgtatgatgcatggcttaatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATGGGTGAAGCTAGACTGATAGATTCAGAGGACATGAGAGCAGCAGCATGGA
                                                tcttc  CT-rich tract
                                            ttaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgatttgcataatctgttttgtcgattcttgattcattataaattattttgctgatgcattcggcttctcttaacgatgccttgcactaaccacaaacatgtatgatgcatggcttaatcttcagGTACAACTTTGATCCTGTAAATGACTGCCCTCTCCCAGGCAGGTTTGAATGGGTGAAGCTAGACTGATAGATTCAGAGGACATGAGAGCAGCAGCATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA