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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtggcgccatacgttctgacacttctttcatcacaggcaatcctttcaccccccccttttcttttgtcatgtaaaaaacaaaaaaacaaaaaccgatcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCTGAACCAAGAGAAGCTCGCCCGGATGCTCGGTAACGTCCAGTCGATGGTC

Basic information

species Zea mays
transcript GRMZM5G862219_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862219_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g06600.2 (Oryza sativa), 3'ss of exon 9
gtacg---tggcgccatacgttctgacacttctttcatcacaggcaatcctttcaccccccccttttcttttgtcatgtaaaaaacaaaaaaacaaaaaccgatcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCTGAACCAAGAGAAGCTCGCCCGGATGCTCGGTAACGTCCAGTCGATGGTC
||| |     |  |   |  || ||    ||  |    ||||    || | ||   | | | ||| | |||||                         ||  || |||| |||||||||||||||||||| ||||| ||||| ||||| |  || ||||||||||||||||| || || |  || ||||| |||||| ||||  ||||| | 
gtatggaccagttcaccattttttggttatttatatgccacatcatatgcattt-tcacactcttcttttttgc------------------------acgaattgaaatagGTATCTGAAAGAAAGGAAACAGTTTGGAGTTCCTCTAGTAGCTTTTCAGCTGAACCAAGAAAAACTTGTGCGAATGCTTGGTAACATCCAAGCGATGCTT
















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|21843242|gb|BQ703823.1|BQ703823
EST:     GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCG                         GTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
genomic: GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGgtacgtggcg ... atcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
EST: gi|91877969|gb|EB407926.1|EB407926
EST:     GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCG                         GTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
genomic: GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGgtacgtggcg ... atcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
EST: gi|87157424|gb|DY402213.1|DY402213
EST:     ATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCG                         GTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
genomic: ATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGgtacgtggcg ... atcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
EST: gi|23357691|gb|BU645340.1|BU645340
EST:     GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCG                         GTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
genomic: GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGgtacgtggcg ... atcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
EST: gi|211159918|gb|FL066976.1|FL066976
EST:     GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCG                         GTATCTGAAAGAWAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
genomic: GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGgtacgtggcg ... atcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
EST: gi|76289157|gb|DV028725.1|DV028725
EST:     GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCG                         GTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
genomic: GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGgtacgtggcg ... atcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
EST: gi|71328257|gb|DR800759.1|DR800759
EST:     GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCG                         GTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
genomic: GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGgtacgtggcg ... atcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
EST: gi|71533929|gb|DR784688.1|DR784688
EST:     GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCG                         GTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
genomic: GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGgtacgtggcg ... atcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
EST: gi|60341737|gb|DN208710.1|DN208710
EST:     ATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCG                         GTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
genomic: ATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGgtacgtggcg ... atcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
EST: gi|26557908|gb|CA830143.1|CA830143
EST:     GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCG                         GTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
genomic: GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGgtacgtggcg ... atcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
EST: gi|93016952|gb|EB642472.1|EB642472
EST:     GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCG                         GTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
genomic: GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGgtacgtggcg ... atcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
EST: gi|71423093|gb|DR805950.1|DR805950
EST:     GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCG                         GTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT
genomic: GCATGGCAACCGGTTGGCATATCAATGGGGGTCTTCGACATGTGCCACCGgtacgtggcg ... atcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccccccttttcttttgtcatgtaaaaaacaaaaaaacaaaaaccgatcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCTGAACCAAGAGAAGCTCGCCCGGATGCTCGGTAACGTCCAGTCGATGGTC
                  atgtaaaaaacaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtggcgccatacgttctgacacttctttcatcacaggcaatcctttcaccccccccttttcttttgtcatgtaaaaaacaaaaaaacaaaaaccgatcgaaacagGTATCTGAAAGAAAGGAAGCAGTTCGGAGTCCCTCTGGCGGCGTTTCAGCTGAACCAAGAGAAGCTCGCCCGGATGCTCGGTAACGTCCAGTCGATGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC