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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagatttgattctaaattaaacgagcagactattttgcagatacatttcttcgctgattgttggcactgacttccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTCATTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAA

Basic information

species Zea mays
transcript GRMZM2G129513_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129513_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 8
---------------------gtgaagatttgattctaa---attaaacgagcagactattttgcaga-tacatttcttcgctgattgttggcactgactt-ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTCATTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAA
                            ||  ||| |||    |  ||  |    ||  || ||  |  ||| ||| ||   |  || ||     ||| || | ||| ||||||||||||||| |||||||| |||||| | || ||||||||||||||||||||||| || || ||||||||||| || || ||||||   ||||||||||
gtgaagatatgattagatattactggctttctattgtaatacttccaattattgtacctttctgtggggtacttttgtttattc-ttattactgatgatttgctctgagtagGTTCCTGATTTTTTGAATGCTAAAATTAACGGGAGACCAGTGAAAGAAGTCATTAAAGACACAAAGTGGTTAGAAGATGAATTCACCAAAACAGTTCAAA
















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|110219294|gb|EC901192.1|EC901192
EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
EST: gi|78089786|gb|DV518160.1|DV518160
EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
EST: gi|32916975|gb|CF021787.1|CF021787
EST:     TGACAAAGTATCAAACGTGACTATTTGGGGGAACCCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAATTTGATGGAAGACCAGTGAAAGAAGTC
genomic: TGACAAAGTATCAAACGTGACTATTTGGGGGAA-CCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
EST: gi|211195515|gb|FL441324.1|FL441324
EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
EST: gi|13198702|gb|BG354504.1|BG354504
EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
EST: gi|211398041|gb|FL283723.1|FL283723
EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGACTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
EST: gi|148971653|gb|EE022376.2|EE022376
EST:     TGACAAAGTATCAAACGTGACTATTTGGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: TGACAAAGTATCAAACGTGACTATTT-GGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
EST: gi|148928691|gb|EC873304.2|EC873304
EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
EST: gi|211395432|gb|FL283722.1|FL283722
EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGACTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
EST: gi|211129427|gb|FL299354.1|FL299354
EST:     GGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: GGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
EST: gi|211195516|gb|FL441325.1|FL441325
EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
EST: gi|30706123|gb|CD059034.1|CD059034
EST:     AAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAACGCCCAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: AAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
EST: gi|74239371|gb|DT647285.1|DT647285
EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
EST: gi|13558383|gb|BG549739.1|BG549739
EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
EST: gi|13490961|gb|BG517725.1|BG517725
EST:     TGACAAANNNNNNNNACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
genomic: TGACAAA-GTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTC
EST: gi|30705491|gb|CD058800.1|CD058800
EST:     ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG                         GTTCCTGATTTC
genomic: ATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTC

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: 44 (upstream exon), 48 (downstream exon)
Score: 38

CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTCATTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 583

CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTCATTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAA


Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 3

CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTCATTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 521

CTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAGgtgaagattt ... ccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTCATTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actattttgcagatacatttcttcgctgattgttggcactgacttccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTCATTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAA
                                    cactgac  putative branch site (score: 521)
                                          cttccctgc  CT-rich tract
            atacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagatttgattctaaattaaacgagcagactattttgcagatacatttcttcgctgattgttggcactgacttccctgcgtagGTTCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTCATTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA