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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtgatcgcggcccgcagcctgcttccatacccgcgcccgtgggggttccgttccatacctgcgtgcatgcggtgctttggtttttaatgctctgctgaattccactgtcgcctctttgtctcacgcgtcctcagGCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAG

Basic information

species Zea mays
transcript GRMZM2G152127_T01
intron # 2
splice site 3'
intron type U2

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|91055766|gb|EB166184.1|EB166184
EST:     AGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAG                         GCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTC
genomic: AGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAGgtcggtgatc ... gcgtcctcagGCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTC
EST: gi|76919428|gb|DV167710.1|DV167710
EST:     AGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAG                         GCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTC
genomic: AGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAGgtcggtgatc ... gcgtcctcagGCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTC
EST: gi|76014959|gb|DT942129.1|DT942129
EST:     AGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAG                         GCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTC
genomic: AGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAGgtcggtgatc ... gcgtcctcagGCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTC
EST: gi|74239653|gb|DT647567.1|DT647567
EST:     AGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAG                         GCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTC
genomic: AGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAGgtcggtgatc ... gcgtcctcagGCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTC
EST: gi|71426983|gb|DR808033.1|DR808033
EST:     AGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAG                         GCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTC
genomic: AGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAGgtcggtgatc ... gcgtcctcagGCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTC
EST: gi|148958182|gb|EC904386.2|EC904386
EST:     AGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAG                         GCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTC
genomic: AGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAGgtcggtgatc ... gcgtcctcagGCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTC
EST: gi|148961536|gb|EE012289.2|EE012289
EST:     AGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAG                         GCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTC
genomic: AGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAGgtcggtgatc ... gcgtcctcagGCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTC

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: 48 (upstream exon), 43 (downstream exon)
Score: 141

CTTGTCCGTGGAGAAGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAGgtcggtgatc ... gcgtcctcagGCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 59

CTTGTCCGTGGAGAAGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAGgtcggtgatc ... gcgtcctcagGCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 39

CTTGTCCGTGGAGAAGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAGgtcggtgatc ... gcgtcctcagGCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

CTTGTCCGTGGAGAAGTGCCCCGACAACAAGATGCTGGGCCGCCGCGAAATCGTCCACGGAAAGgtcggtgatc ... gcgtcctcagGCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttaatgctctgctgaattccactgtcgcctctttgtctcacgcgtcctcagGCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAG
                                      gtctcac  putative branch site (score: 169)
                                              cgtcctc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggtgatcgcggcccgcagcctgcttccatacccgcgcccgtgggggttccgttccatacctgcgtgcatgcggtgctttggtttttaatgctctgctgaattccactgtcgcctctttgtctcacgcgtcctcagGCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT