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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccattttagtttaactgatataggagtaaaaacatttcaattttaccttagcaaccacttgcaaatgaatggctactgaaacctttcgtccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATGGGGTGAAGGTCCTAGCCTTGACAATGGCTACGCTGTCGCTGGAGTGACT

Basic information

species Zea mays
transcript GRMZM2G130034_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130034_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os12g40550.1 (Oryza sativa), 3'ss of exon 11
taccattttagtttaactgatataggagtaaaaacatttcaattttaccttagcaaccacttgcaaa-tgaatggctactgaaa--cctttcgtccc--tttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATGGGGTGAAGGTCCTAGCCTTGACAATGGCTACGCTGTCGCTGGAGTGACT
    | ||||    |||  ||||    || ||   || | || || |   ||  |||| | |  ||| ||||| || |||||||    | || | |   || ||||||||||||||||||| || || ||||| ||||| |||||||||||||| || |||||||| || |||||| ||||||| |   | || ||| |||||  
--taaattta---caacgcatatcctggtgaatgaatataaagttcaaactaataacctcctataaaatgaattgccactgaaaaagttatccttctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACGGTGTGAAGGTGCTTGCCTTGGCAATGGCCAGATTATCCCTGCAGTGAGC
















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|86468217|gb|DY234587.1|DY234587
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCCCAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|86473058|gb|DY239428.1|DY239428
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|31362362|gb|CD446719.1|CD446719
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|88749671|gb|DY533812.1|DY533812
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|33466598|gb|CF243647.1|CF243647
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|24768371|gb|CA403500.1|CA403500
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|78022951|gb|DV491338.1|DV491338
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|50333648|gb|CO528774.1|CO528774
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|211502326|gb|FL069735.1|FL069735
EST:     AGTATCACCCAAATGGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGGCCGGGAGGAGTATGCATTCACCCGAGGACATGGCGA
genomic: AGTATCACC-AA-TGGG-TATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAG-CCGG-AGGAGTATGCAT-CACCCGAGGACATGGCGA
EST: gi|71775246|gb|DR973124.1|DR973124
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|211502325|gb|FL069734.1|FL069734
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|148936612|gb|EC880735.2|EC880735
EST:     TCCCTGTTACAAAG                         GTTACAGCCACAACCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: TCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|76288907|gb|DV028475.1|DV028475
EST:     TTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: TTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|91874397|gb|EB404354.1|EB404354
EST:     AGTATCACCAATGGGTATGATTTTCATTCCCTGTTACAAAG                         GTTACAGCCCCAAGCCGGAGGGGTATGCATCCCCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|30087001|gb|CB885209.1|CB885209
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|76288906|gb|DV028474.1|DV028474
EST:     TTCATTCCCTGTTACAAAG                         GTTACAGCCCCAAGCCGGAGGAGTATGCATCCCCCGAGGACATGGCGAATG
genomic: TTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|71441172|gb|DR822222.1|DR822222
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|148944451|gb|EC889566.2|EC889566
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|71305488|gb|DR788881.1|DR788881
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|78107617|gb|DV526035.1|DV526035
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|5714250|gb|AI944235.1|AI944235
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|148983477|gb|EE029495.2|EE029495
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCCCAAGCCGGAGGAGTATGCATCCCCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|71427277|gb|DR808327.1|DR808327
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|86468218|gb|DY234588.1|DY234588
EST:     AGTATCACCAAGGGGTATGATCTTCTTTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|149103752|gb|EE289158.2|EE289158
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCCCAAGCCGGAGGAGTATGCATCCCCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|50324879|gb|CO520005.1|CO520005
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
EST: gi|50323472|gb|CO518598.1|CO518598
EST:     AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAG                         GTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG
genomic: AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATG

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: 47 (upstream exon), 44 (downstream exon)
Score: 98

AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATGGGGTGAAGGTCCTAGCCTTGACAATGGCTACGCTGTCGCTGGAGTGACT


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 137

AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATGGGGTGAAGGTCCTAGCCTTGACAATGGCTACGCTGTCGCTGGAGTGACT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 104

AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATGGGGTGAAGGTCCTAGCCTTGACAATGGCTACGCTGTCGCTGGAGTGACT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 55

AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctc ... tccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATGGGGTGAAGGTCCTAGCCTTGACAATGGCTACGCTGTCGCTGGAGTGACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccttagcaaccacttgcaaatgaatggctactgaaacctttcgtccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATGGGGTGAAGGTCCTAGCCTTGACAATGGCTACGCTGTCGCTGGAGTGACT
                                      cctttcgtccctttc  CT-rich tract
                   aaatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taccattttagtttaactgatataggagtaaaaacatttcaattttaccttagcaaccacttgcaaatgaatggctactgaaacctttcgtccctttcagGTTACAGCCACAAGCCGGAGGAGTATGCATCACCCGAGGACATGGCGAATGGGGTGAAGGTCCTAGCCTTGACAATGGCTACGCTGTCGCTGGAGTGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - -aaaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - -caaccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctactg