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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgttgctttcctcctcagctctaacctcaatacctccatgttatctcatttctcacattggaggtactccttatttgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG

Basic information

species Zea mays
transcript GRMZM2G107082_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 3
------------------------gtacttgttgctttcctcctcagctctaacctc--aatacctccatgttatctcatttctcacattggaggtactccttatttgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG
                        |   ||||  ||       |    |  |       | ||| || ||  | || |||  || | | |    | |||    ||||  | || ||||||| |||||||||||||| |||||||||||||| ||||| ||||||| ||
gtatttgtcctgttaaaattatttgcctttgtacctcattcagttgatttcatttgaggagtacttctat-ctgtcacatg-cttataataattgaactgtacatttcgtcattagGCACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTCTTCCAAG

upper sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g47330.1 (Oryza sativa), 3'ss of exon 3
------------------gtacttgttgcttt--cctcctcagct---ctaacctc---aatacctccatgttatctcatttctcacattggaggtactccttatttgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG
                   || |||    | |  | |  |||| |    | |  |    | ||| ||||| || || |||  || | | |    | |||    ||||    |||||||||| |||||||||||||| |||||||||||||| ||||| || |||| ||
gtatttgtactgttaaaattatttgccattgtaccttgttcagttgatttcatttgaggagtacttccat-ttgtcacatg-cttataataattgaactgtacatttcgacatcagGCACGTGGAAAAATTGGTGATTTCATTAAAGGAGTCTTTGCTGTTTTCCAAG
















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|211124407|gb|FL002541.1|FL002541
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACSCGGAAAAAWTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|32928214|gb|CF033026.1|CF033026
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|89759015|gb|DY687974.1|DY687974
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|14243577|gb|BG841276.2|BG841276
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|32846052|gb|CD985733.1|CD985733
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGTAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|211124415|gb|FL002549.1|FL002549
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|33093807|gb|CF053801.1|CF053801
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|32941416|gb|CF046235.1|CF046235
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|148996106|gb|EE035369.2|EE035369
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|71769087|gb|DR967024.1|DR967024
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|211123625|gb|FL002524.1|FL002524
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAACATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|211123624|gb|FL002523.1|FL002523
EST:     GACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: GACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|33100741|gb|CF060701.1|CF060701
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCGACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCTGTCTTCCAA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|211122852|gb|FL002520.1|FL002520
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTG
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTG
EST: gi|89758437|gb|DY687616.1|DY687616
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|6012698|gb|AW062135.1|AW062135
EST:     CAATGACGTCTGATTCATGTGNTCCTTTGATTGCGACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCTGTCTTCCAA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|6022461|gb|AW067494.1|AW067494
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCGACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGC
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGC
EST: gi|148953532|gb|EE153041.2|EE153041
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|33094495|gb|CF054489.1|CF054489
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|211125184|gb|FL002552.1|FL002552
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         G-ACGCGGAAAA-TTGGTGACT
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACT
EST: gi|32928697|gb|CF033509.1|CF033509
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|32858269|gb|CD997950.1|CD997950
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGG--AAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCNCC
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTT--CC
EST: gi|148941766|gb|EC886727.2|EC886727
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA
EST: gi|33104066|gb|CF064026.1|CF064026
EST:     CAATGACGTCTGATTCATGTGCTCCTTTGATTGCGACCCTTCCATTGGAG                         GCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCTGTCTTCCAA
genomic: CAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTA

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: 417

TGAGGAGAACTGGGACAAGGTTAAGACTATTTTCCTTCCTACTGAGAAGCCAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 635

TGAGGAGAACTGGGACAAGGTTAAGACTATTTTCCTTCCTACTGAGAAGCCAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 452

TGAGGAGAACTGGGACAAGGTTAAGACTATTTTCCTTCCTACTGAGAAGCCAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 2151

TGAGGAGAACTGGGACAAGGTTAAGACTATTTTCCTTCCTACTGAGAAGCCAATGACGTCTGATTCATGTGCTCCTTTGATTGCAACCCTTCCATTGGAGgtacttgttg ... tgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacctccatgttatctcatttctcacattggaggtactccttatttgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG
                   ttctcac  putative branch site (score: 2151)
                                    ctccttattt  putative PPT
                                        ttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgttgctttcctcctcagctctaacctcaatacctccatgttatctcatttctcacattggaggtactccttatttgctgatcagGCACGCGGAAAAATTGGTGACTTCATTAAAGGAGTGTTTGCCGTCTTCCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG