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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtttactgaggacaactacgtgctttgtctgttacgccatgttttggtacatcgaactttagtaacgatgctatatttggcggtttatcatgcagGGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTCTGCAGCTGCATGGGTCGTTTCAGAACACAGAAAAACGGCAGGGTGATCT

Basic information

species Zea mays
transcript GRMZM5G855347_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G855347_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g08070.1 (Oryza sativa), 3'ss of exon 15
------------------gta---atgtttactga--ggacaactacgtgctttgtctg--ttacgccat-gttttggtacatcgaactttagtaacgatgctatatttggcggtttatcatgcagGGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTCTGCAGCTGCATGGGTCGTTTCAGAACACAGAAAAACGGCAGGGTGATCT
                  |||   || |  ||         | |    || ||||| ||  |  | ||||  | ||   |    || ||||| ||  |    | |   ||  |||  |||||| |||||| ||||||||||| ||||| || |||||||||||||||||||| ||||| || || ||||| || |||||||  || |||||||  | ||  |||||
gtacaatataccgctattgtatgcatctccaccatttcagtatccgtatggtttgtttgcatcccaccattatcttaaaattatgagctttaatattgtctttgt---tgatggt--atcatgtagGGGGATTGATGGCCCTGAGCTCGATTTTTGTTGTCAGCAATTCTTTACTTCTACAACTACATGGATCATTTCAGAGTACGGAAAAACAACGGGAAGATCT
















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|5714129|gb|AI944114.1|AI944114
EST:     TGCTGCCCACAATATGATTTCCCCATGACACCATCTCTCTCAG                         GGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC
genomic: TGCTG-CCACAATATGATTTCGCCATGACACCATCTCTCTCAGgtaatgttta ... tatcatgcagGGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC
EST: gi|211313984|gb|FL435296.1|FL435296
EST:     TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAG                         GGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC
genomic: TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAGgtaatgttta ... tatcatgcagGGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC
EST: gi|211410041|gb|FL464377.1|FL464377
EST:     TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAG                         GGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC
genomic: TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAGgtaatgttta ... tatcatgcagGGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC
EST: gi|60353203|gb|DN220176.1|DN220176
EST:     TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAG                         GGGGGTTGATGGCCCTTAGCTCAATCTTTGTTG
genomic: TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAGgtaatgttta ... tatcatgcagGGGGGTTGATGGCCCTTAGCTCAATCTTTGTTG
EST: gi|32835068|gb|CD974746.1|CD974746
EST:     TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAG                         GGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC
genomic: TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAGgtaatgttta ... tatcatgcagGGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC
EST: gi|211367137|gb|FL432362.1|FL432362
EST:     TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAG                         GGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC
genomic: TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAGgtaatgttta ... tatcatgcagGGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC
EST: gi|5525756|gb|AI861649.1|AI861649
EST:     TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAG                         GGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC
genomic: TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAGgtaatgttta ... tatcatgcagGGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC
EST: gi|60358034|gb|DN225007.1|DN225007
EST:     TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAG                         GGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC
genomic: TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAGgtaatgttta ... tatcatgcagGGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC
EST: gi|32832471|gb|CD972149.1|CD972149
EST:     TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAG                         GGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC
genomic: TGGAGTGCTGCTGCCACAATATGATTTCGCCATGACACCATCTCTCTCAGgtaatgttta ... tatcatgcagGGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttggtacatcgaactttagtaacgatgctatatttggcggtttatcatgcagGGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTCTGCAGCTGCATGGGTCGTTTCAGAACACAGAAAAACGGCAGGGTGATCT
                   tagtaac  putative branch site (score: 1)
                               tatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtttactgaggacaactacgtgctttgtctgttacgccatgttttggtacatcgaactttagtaacgatgctatatttggcggtttatcatgcagGGGGGTTGATGGCCCTTAGCTCAATCTTTGTTGTCAGCAATTCTTTGCTTCTGCAGCTGCATGGGTCGTTTCAGAACACAGAAAAACGGCAGGGTGATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC