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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttggcaagctgttgcctgatttaggagcttcaccaagcagtgctcccttattctgtttttgttatcccttgtgaccttatattgtatctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCACCAACATCTACTGCACCTGCAGCCAACCAAGAACCTACCACTGCTGCTCC

Basic information

species Zea mays
transcript GRMZM2G127101_T01
intron # 1
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|211455129|gb|FK981377.1|FK981377
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|148932108|gb|EC875499.2|EC875499
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|149094649|gb|EE180188.2|EE180188
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|211452997|gb|FK981360.1|FK981360
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|91874891|gb|EB404848.1|EB404848
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|149079049|gb|EE167936.2|EE167936
EST:     ATCTACAAGGGCCGGATCTTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACCATGGTACGTGGTGCTGTGCTATCC
genomic: ATCTACAAGGGCCGGATCTT-GAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCAC-ATGGTACGTGGTGCTGTGCTATCA
EST: gi|211455131|gb|FK981379.1|FK981379
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|211453000|gb|FK981363.1|FK981363
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|211452996|gb|FK981359.1|FK981359
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|78107356|gb|DV525774.1|DV525774
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|211450863|gb|FK981351.1|FK981351
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACMGACCATACAATCCACATGGTACGTGGTG
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTG
EST: gi|211450867|gb|FK981355.1|FK981355
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|91877131|gb|EB407088.1|EB407088
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|148983366|gb|EE029352.2|EE029352
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|149098089|gb|EE184042.2|EE184042
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|148960785|gb|EE011445.2|EE011445
EST:     ATCTACAAGGGCCGGATCTTGGAGGACGAGCAAACCCTAGCCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGGGCTGTGCT
genomic: ATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCC-AGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCT
EST: gi|148987252|gb|EE031087.2|EE031087
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|149084597|gb|EE174071.2|EE174071
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|71446627|gb|DR827677.1|DR827677
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|211450860|gb|FK981348.1|FK981348
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCCATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|211455126|gb|FK981374.1|FK981374
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|76916497|gb|DV166415.1|DV166415
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|71434964|gb|DR816014.1|DR816014
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|71318698|gb|DR796107.1|DR796107
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|211455127|gb|FK981375.1|FK981375
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|211419239|gb|FK977455.1|FK977455
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|211455128|gb|FK981376.1|FK981376
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|148943115|gb|EC888173.2|EC888173
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
EST: gi|211450864|gb|FK981352.1|FK981352
EST:     GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACG                         GTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC
genomic: GATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCAC

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), 48 (downstream exon)
Score: 117

AAGGCGATCGTCGCCCACAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCACCAACATCTACTGCACCTGCAGCCAACCAAGAACCTACCACTGCTGCTCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 119

AAGGCGATCGTCGCCCACAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCACCAACATCTACTGCACCTGCAGCCAACCAAGAACCTACCACTGCTGCTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

AAGGCGATCGTCGCCCACAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCACCAACATCTACTGCACCTGCAGCCAACCAAGAACCTACCACTGCTGCTCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 114

AAGGCGATCGTCGCCCACAGCTGCGACGTGCCGGCGCCGCAGCAGCGGCTGATCTACAAGGGCCGGATCTTGAAGGACGAGCAAACCCTAGCCAGCTACGgtgcgtgctt ... ctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCACCAACATCTACTGCACCTGCAGCCAACCAAGAACCTACCACTGCTGCTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcccttattctgtttttgttatcccttgtgaccttatattgtatctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCACCAACATCTACTGCACCTGCAGCCAACCAAGAACCTACCACTGCTGCTCC
                                          tatcttttt  CT-rich tract
                                  ttatattgtatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttggcaagctgttgcctgatttaggagcttcaccaagcagtgctcccttattctgtttttgttatcccttgtgaccttatattgtatctttttaaagGTGTGGAGACAGACCATACAATCCACATGGTACGTGGTGCTGTGCTATCACCAACATCTACTGCACCTGCAGCCAACCAAGAACCTACCACTGCTGCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - gctgttg
- - - - - - - - - ctgattt
- - - - - - - - - - - - - - -gcttcac
- - - - - - - - - - - - - - - - - - caagcag