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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATTGCTCATGGGGTGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaatagtattttttgtgttgattgaacatccattggattttcatatagttgcttgagagggactaattaattatattttgtccggctgtgttcag

Basic information

species Zea mays
transcript GRMZM2G134396_T03
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134396_T03 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os07g49270.1 (Oryza sativa), 5'ss of exon 16
CGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATTGCTCATGGGGTGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaatagt------------------attttttgtgttgattgaacatccattgga----ttttcatatagttgcttgagag----ggactaattaattatattttgtccggctgtgttcag
 ||||| ||||||||||||||||||||||| ||||| |||||||| ||||| ||  ||||||| |||||||| || ||||| |||||||| || |||||||| | || || |                  |||||||  |   |      ||| |||| |    | |  || | |||   |  ||     | |  || |||  || ||||||  | || |  | ||
TGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATTGCTCACGGGGTTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATTACCTAGCTCAGgtaactagtattttgtgttcattcctcatcatttttttagcgcaacagctatcaattgaacacctatcaattttgttttctcggatctttgaataaactaaccatcttttgtttgcctataattag
















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|14203330|gb|BG837007.1|BG837007
EST:     TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAG                         ATTGGTCTAGCAATGTCTCCCTTGAGTAACAACTCACTGTTTATCGACTAT
genomic: TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
EST: gi|67028452|gb|CO457201.1|CO457201
EST:     TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAG                         ATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
genomic: TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
EST: gi|21987227|gb|BQ778755.1|BQ778755
EST:     TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAG                         ATTGGTCTAGCAATGTCTCCCTTGAGTAACAACTCACTGTTTATCGACTAT
genomic: TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
EST: gi|74237693|gb|DT645607.1|DT645607
EST:     TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAG                         ATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
genomic: TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
EST: gi|71299097|gb|DR785545.1|DR785545
EST:     CCTGTACTTCAGTACCTGTATTATCTTGCTCAG                         ATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
genomic: CCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
EST: gi|149090162|gb|EE179462.2|EE179462
EST:     TCAGTACCTGTATTATCTTGCTCAG                         ATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
genomic: TCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
EST: gi|211424036|gb|FL301688.1|FL301688
EST:     TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAG                         ATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
genomic: TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
EST: gi|33090962|gb|CF050956.1|CF050956
EST:     TACCTGTATTATCTTGCTCAG                         ATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
genomic: TACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
EST: gi|71299098|gb|DR785546.1|DR785546
EST:     TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAG                         ATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
genomic: TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
EST: gi|32931798|gb|CF036610.1|CF036610
EST:     ACCTGTATTATCTTGCTCAG                         ATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
genomic: ACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
EST: gi|211424037|gb|FL301689.1|FL301689
EST:     TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAG                         ATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
genomic: TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
EST: gi|211424038|gb|FL301690.1|FL301690
EST:     TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAG                         ATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
genomic: TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
EST: gi|78121620|gb|DV540004.1|DV540004
EST:     TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAG                         ATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
genomic: TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
EST: gi|211424039|gb|FL301691.1|FL301691
EST:     TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAG                         ATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT
genomic: TGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 176

CGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATTGCTCATGGGGTGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTATCATCGGAACCCTTTCCCAACATTTTTCTTAAGGGGTCTTAACGTGTCTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 122

CGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATTGCTCATGGGGTGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTATCATCGGAACCCTTTCCCAACATTTTTCTTAAGGGGTCTTAACGTGTCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 308

CGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATTGCTCATGGGGTGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTATCATCGGAACCCTTTCCCAACATTTTTCTTAAGGGGTCTTAACGTGTCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

CGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATTGCTCATGGGGTGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaata ... ctgtgttcagATTGGTCTAGCAATGTCTCCCTTAAGTAACAACTCACTGTTTATCGACTATCATCGGAACCCTTTCCCAACATTTTTCTTAAGGGGTCTTAACGTGTCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATTGCTCATGGGGTGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATTATCTTGCTCAGgttagtaatagtattttttgtgttgattgaacatccattggattttcatatagttgcttgagagggactaattaattatattttgtccggctgtgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA