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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattcatgctttcgatgtacctcacagatctcagttgcctccatattaattgtaccagccatttttatgtgaaagggagacgtttttctactatattgtcaatcataacagccattattttcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG

Basic information

species Zea mays
transcript GRMZM2G034083_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034083_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g37870.1 (Oryza sativa), 3'ss of exon 5
gtatgattcatgctttcgatgtacctcacagatctcagttgcctccatattaattgtaccagccatttttatgtgaaagggagacgtttttctactatattgtcaatcataacagccattattttcatg-tacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG
                                      |          ||  || | | |||     |  |||  |    |  | |||  | |      ||    ||||   | |||    || ||||  | |||||||| || |||  ||| || || || || |||||||| ||||| ||||| ||||| ||||||||||||||||||||||||
-----------------------------------gtatgattcaggcttttttttttctagcttacatagtgtccagttcaatcctttcacca------tgcttgtcatgctaaccagagcttccatggcatagGTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTCTGAAAGCTTTATCCATGAACTGGATGAGAAG

upper sequence: GRMZM2G034083_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 3'ss of exon 6
gtatgattcatgctttcgatgtacctcacagatctcagttgc-ctccatattaattgtaccagccatttttatgtgaaagggagacgtttttctactatattgtcaatcataacagccattattttcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG
                             | | ||  |||   ||  | | || |     |||  ||||| |  |       | |   |||   | | | || || ||          ||| || |  |  |||||||||||||||||| |||||| || || ||||||||||| || || ||| | ||  | |  || ||     ||||||| |||
---------------------------gtatacctttgttattctgaaaaatactcaagtcagaaattttcagttact----acatactttcagagtgtcttatctata--------tattgttatgcta-acagGTGGGGCAATATTGAGTTTCCGCTGCCTTTTGGAAGAGTACTAAGCCCCACAGAGGGCTACATTCACTCGTTGGATGAAAAG
















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|32848515|gb|CD988196.1|CD988196
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|67023264|gb|CO452013.1|CO452013
EST:     GAGAGGTGAACTAGATGACACAGCTGCTTTCACAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|31356652|gb|CD441009.1|CD441009
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|31357444|gb|CD441801.1|CD441801
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|211020101|gb|FL063974.1|FL063974
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|18964714|gb|BM661164.1|BM661164
EST:     TTCAAAAACTTCAAT-A                         GTGGGGCAATA-TGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: TTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|60353107|gb|DN220080.1|DN220080
EST:     GACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAACATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|18964715|gb|BM661165.1|BM661165
EST:     GATATGAGAGGAGAACTAGATGACNCAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|22490798|gb|BU050721.1|BU050721
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|67025367|gb|CO454116.1|CO454116
EST:     CTAGATGACTCCCCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: CTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|67010398|gb|CO439147.1|CO439147
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCANAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|7238111|gb|AW573333.1|AW573333
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAACATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|44901489|gb|CK828034.1|CK828034
EST:     AGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAACA-TGTTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCT
genomic: AGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTG-TGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCT
EST: gi|19058295|gb|BM736962.1|BM736962
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAACCTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|78103680|gb|DV522108.1|DV522108
EST:     ATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: ATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|31353311|gb|CD437668.1|CD437668
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|13150060|gb|BG320382.1|BG320382
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|13150055|gb|BG320377.1|BG320377
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|31354936|gb|CD439293.1|CD439293
EST:     GATCTTAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTTCCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|31355046|gb|CD439403.1|CD439403
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATT
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATT
EST: gi|19057819|gb|BM736486.1|BM736486
EST:     CTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: CTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|87151765|gb|DY396554.1|DY396554
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|67042517|gb|CO468772.1|CO468772
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAACATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|32859101|gb|CD998782.1|CD998782
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|33104123|gb|CF064083.1|CF064083
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|148955951|gb|EC901669.2|EC901669
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAA-CTTCAATAA                         GTGGGGCAATATT
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATT
EST: gi|37401585|gb|CF638160.1|CF638160
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAACATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
EST: gi|148986293|gb|EE030028.2|EE030028
EST:     ATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTNCA-TAA                         GTGGGGCAATATTG
genomic: ATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTT-CAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTG
EST: gi|67016541|gb|CO445290.1|CO445290
EST:     GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAA                         GTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC
genomic: GATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTC

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: 344

TTCTTGAGATGAACCCATTCACCTTGGTAAATGGTGAACCGTATCCTCTGGATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 695

TTCTTGAGATGAACCCATTCACCTTGGTAAATGGTGAACCGTATCCTCTGGATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 673

TTCTTGAGATGAACCCATTCACCTTGGTAAATGGTGAACCGTATCCTCTGGATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 905

TTCTTGAGATGAACCCATTCACCTTGGTAAATGGTGAACCGTATCCTCTGGATATGAGAGGAGAACTAGATGACACAGCTGCTTTCAAAAACTTCAATAAgtatgattca ... tcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagacgtttttctactatattgtcaatcataacagccattattttcatgtacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG
                           tcataac  putative branch site (score: 905)
                                       ttattttc  putative PPT
       tttttctactatatt  TA-rich tract