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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcgctgctttgttctatttcagtcgctgtttgtttcccattgctgcaatgttatctgttgcaaacctctgttaatattttgatttgaactttcgaaggctatctggtaatgtttgaccgtaatggtgcttgttttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCTCCGGACAAGAAACCGGCTCGCCTACCT

Basic information

species Zea mays
transcript GRMZM5G828229_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G828229_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g05570.2 (Oryza sativa), 3'ss of exon 3
gtatcgctgctttgttctatttcagtcgctgtttgtttcccattgctgcaatgttatctgttgcaaacctctgttaatattttgatttgaactttcgaaggctatctggtaatgtttgaccgtaatggtgcttgttttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCTCCGGACAAGAAACCGGCTCGCCTACCT
                       |  || |||||| |   ||||| |   |||| |     |||||   | | || ||    ||||||    ||| ||    |||  | |   |||||            |||  | | |||||| |   ||| ||||| ||||| |||||  |||| || ||||||||||| ||||| |||||||| || ||||| ||||||
---------------------gaatgcgttgtttggt---cattgttctcatgtaac----tgcaa---tgtattgattggctgatttttttttttgagatttat--gatggggtttg------------cttactgtaatgcagGCGTATCCGCCATATGAGCGACCAGCACTGACAAAGGGCTATCTTTTCCCTCCAGACAAGAAGCCTGCTCGTCTACCT
















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|211072897|gb|FL344949.1|FL344949
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|211467623|gb|FL333695.1|FL333695
EST:     TCGTGGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|211399942|gb|FL360079.1|FL360079
EST:     TCGTGGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|22545888|gb|BU098127.1|BU098127
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCGTCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|149075601|gb|EE164139.2|EE164139
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|211149413|gb|FL321993.1|FL321993
EST:     TCGTGGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|211306680|gb|FL364491.1|FL364491
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|211333832|gb|FL364099.1|FL364099
EST:     TCGTGGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|211075749|gb|FL351701.1|FL351701
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAG
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAG
EST: gi|148990927|gb|EE032350.2|EE032350
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|211270379|gb|FL351863.1|FL351863
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|21621068|gb|BQ619074.1|BQ619074
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|87156678|gb|DY401467.1|DY401467
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCGTCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|148931379|gb|EC874296.2|EC874296
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|148931941|gb|EC875173.2|EC875173
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|148995891|gb|EE035131.2|EE035131
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|78103956|gb|DV522374.1|DV522374
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|211267804|gb|FL345561.1|FL345561
EST:     TCGTGGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|211157246|gb|FL334279.1|FL334279
EST:     TCGTGGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|211098259|gb|FL316228.1|FL316228
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTT
EST: gi|211511443|gb|FL329917.1|FL329917
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTT
EST: gi|211043461|gb|FL324043.1|FL324043
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|148957061|gb|EC903025.2|EC903025
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|19436377|gb|BM952787.1|BM952787
EST:     TCGTGGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|211297775|gb|FL337585.1|FL337585
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTYCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|211004058|gb|FL319209.1|FL319209
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|88750901|gb|DY535042.1|DY535042
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|211472696|gb|FL333736.1|FL333736
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|213168062|gb|FM185604.1|FM185604
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCGTCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|26558495|gb|CA830730.1|CA830730
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCGTCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|6587631|gb|AW244949.1|AW244949
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCGTCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
EST: gi|7242278|gb|AW574464.1|AW574464
EST:     TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAG                         CCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT
genomic: TCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCT

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: 224

GTATGTGATCGTCGGGGGAGGGAACGCTGCGGGTTACGCCGCCAGGACGTTCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCTCCGGACAAGAAACCGGCTCGCCTACCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 145

GTATGTGATCGTCGGGGGAGGGAACGCTGCGGGTTACGCCGCCAGGACGTTCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCTCCGGACAAGAAACCGGCTCGCCTACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

GTATGTGATCGTCGGGGGAGGGAACGCTGCGGGTTACGCCGCCAGGACGTTCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCTCCGGACAAGAAACCGGCTCGCCTACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

GTATGTGATCGTCGGGGGAGGGAACGCTGCGGGTTACGCCGCCAGGACGTTCGTCGAGCATGGCATGGCTGACGGCCGCCTTTGCATCGTCTCCAAGGAGgtatcgctgc ... tttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCTCCGGACAAGAAACCGGCTCGCCTACCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttcgaaggctatctggtaatgtttgaccgtaatggtgcttgttttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCTCCGGACAAGAAACCGGCTCGCCTACCT
                       gtttgac  putative branch site (score: 127)
                                        cttgttttc  putative PPT
                   taatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcgctgctttgttctatttcagtcgctgtttgtttcccattgctgcaatgttatctgttgcaaacctctgttaatattttgatttgaactttcgaaggctatctggtaatgtttgaccgtaatggtgcttgttttcatgcagCCAGTTCCACCATACGAGCGGCCAGCCTTGACCAAAGGCTATCTTTTTCCTCCGGACAAGAAACCGGCTCGCCTACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA