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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctgcattcgctgacacttctacggttctcccacagaattgcaacattgagcatctgacatctctaacccttctcctgtttcaaatcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG

Basic information

species Zea mays
transcript GRMZM2G126765_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126765_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g53160.1 (Oryza sativa), 3'ss of exon 3
gtacctgcattcgctgacacttctacggttctcccacagaattgcaacattgagcatctgacatctctaacccttctcctgtttcaaatcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
||| |||| |   |  | |  | | |  |    |   | |||| || ||   |  |||||   | |||||| ||| || | ||    |||  ||||||||| || || || ||||| ||||||||||||||||||||||||
gtatctgcctctacaaagatatatccaatgtctc---aaaatttcatcac--actatctg---tatctaactcttatcgtttt---gatcaattcagACGTAAGGAATCAACCGGTGCTCATCCACTGCAAGAGAGGCAAG
















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|18174219|gb|BM349607.1|BM349607
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|31558116|gb|CD527328.1|CD527328
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18170840|gb|BM340680.1|BM340680
EST:     GGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: GGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|31558117|gb|CD527329.1|CD527329
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18167985|gb|BM337825.1|BM337825
EST:     AGGCGCTCAAAGTTGTCCTTG                         ACGTGAAAAACCAACCGGTCCCTCATCCACTGCAAGAGAGGCAAG
genomic: AGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGT-CCTCATCCACTGCAAGAGAGGCAAG
EST: gi|78093024|gb|DV521398.1|DV521398
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCTGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18163480|gb|BM333319.1|BM333319
EST:     CGTCCACATCCCCAAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18166488|gb|BM336327.1|BM336327
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18176420|gb|BM351381.1|BM351381
EST:     TCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: TCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|37388689|gb|CF631556.1|CF631556
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18167235|gb|BM337074.1|BM337074
EST:     GAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: GAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18161992|gb|BM331831.1|BM331831
EST:     GCGCTCAAAGTTGTCCTTA                         ACGTGAGAAACCAACCGGTCCTCATCCAATGCAAGAGAGGCAAG
genomic: GCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18175417|gb|BM350752.1|BM350752
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18168798|gb|BM338638.1|BM338638
EST:     CGATCCGGNAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|28986278|gb|CB351056.1|CB351056
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18167555|gb|BM337394.1|BM337394
EST:     CGTCCACATCCCCAAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|17929863|gb|BM266823.1|BM266823
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18162825|gb|BM332664.1|BM332664
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|16921811|gb|BM075311.1|BM075311
EST:     TCCACATCCCCGAAGAAACGATCCGGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: TCCACATCCCCGAAGAAACGATCC-GGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|17930139|gb|BM267099.1|BM267099
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18170685|gb|BM340525.1|BM340525
EST:     AAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: AAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|16920825|gb|BM074849.1|BM074849
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18168498|gb|BM338338.1|BM338338
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18167487|gb|BM337326.1|BM337326
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|76283506|gb|DV023074.1|DV023074
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18170266|gb|BM340106.1|BM340106
EST:     TCCACATCCCCGAAAAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTAAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: TCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|78093023|gb|DV521397.1|DV521397
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCTGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18172194|gb|BM347582.1|BM347582
EST:     CACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCATCATCCACTGCAAGAGAGGCAAG
genomic: CACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18164282|gb|BM334121.1|BM334121
EST:     CGCTCAAAGTTGTCCTTG                         ACGT-AAAAACACAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAAC-CAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|17929626|gb|BM266586.1|BM266586
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18168877|gb|BM338717.1|BM338717
EST:     CACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|18167709|gb|BM337549.1|BM337549
EST:     TCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: TCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
EST: gi|16922990|gb|BM075982.1|BM075982
EST:     CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG                         ACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
genomic: CGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG

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 3 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 54

AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG


Block sizes: 33 (upstream exon), 44 (downstream exon)
Score: 20

AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 44

AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTGgtacctgcat ... atcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaacattgagcatctgacatctctaacccttctcctgtttcaaatcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG
                      ctctaac  putative branch site (score: 44)
                                              tcgtttc  putative PPT
                                       tttcaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctgcattcgctgacacttctacggttctcccacagaattgcaacattgagcatctgacatctctaacccttctcctgtttcaaatcgtttcagACGTGAGAAACCAGCCGGTCCTCATCCACTGCAAGAGAGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG