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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaaaatacttcattaaagcaccattgcacacatcaaagtgttatgtgttgtgtcaaccatagtaagcaataagctgttctgattgtcataactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAGGAAGAGAATCAAGCTCAGTGCTGAGAAAGCTATCTTCATCTTTGTGAAG

Basic information

species Zea mays
transcript GRMZM2G076826_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G076826_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g53240.2 (Oryza sativa), 3'ss of exon 5
---caaaaatact-tcattaaagcaccattgcacacatcaaagtgt-tatgtgttgtgtcaaccatagtaagcaataagctgttctgattgtcataactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAGGAAGAGAATCAAGCTCAGTGCTGAGAAAGCTATCTTCATCTTTGTGAAG
| ||| | | | | || | ||| | | | ||| | ||| || | | | || || ||||| || ||| | |||||||| ||||||||||||||||| ||||| || || || ||||||||| ||||| | |||||||||||| |||||||||| ||||||||||||||||||
gctcgaaacttttgttgctctgaaactttaatacatgttacatcaagtatcaatcaatattaccgta-tcatccttagtagcttatgattttc-taa---tatagGTACCTGGTCCCTGCTGATCTTACCGTTGGGCAGTTTGTCTATGTTGTTCGGAAGCGGATCAAGCTCAGTCCTGAGAAAGCAATCTTCATCTTTGTGAAG

upper sequence: GRMZM2G076826_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 4
caaaaatactt---cattaaagcaccattgcacacatcaaagtgttatgtgttgtgtcaaccatagtaagcaataagctg--ttctgattgtcataactt-tgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAGGAAGAGAATCAAGCTCAGTGCTGAGAAAGCTATCTTCATCTTTGTGAAG
| || || |||| | | | | | ||| | | ||| | | || || | || ||| ||| | | |||| | ||||| || || || ||||||||||| || ||||| || || || ||||| | ||||||| |||||||| ||||||||||| ||||| ||||| ||||| |||
-tagtatgttttcacattcgattattgtcttatatggtaaattcct----gtttagctgattttatcaaatattatcctgagttcctact-tcatgatcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCGGAAGAGGATCAAGCTTAGTGCTGAGAAGGCTATTTTCATTTTTGTCAAG
















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|211035126|gb|FL190210.1|FL190210
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|211509914|gb|FL437411.1|FL437411
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|18165025|gb|BM334870.1|BM334870
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGGCAAGAAAAA                         GTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|71441162|gb|DR822212.1|DR822212
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|91052588|gb|EB163006.1|EB163006
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|211192317|gb|FL065114.1|FL065114
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTGGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|18169711|gb|BM339551.1|BM339551
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|71434664|gb|DR815714.1|DR815714
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|211194714|gb|FL065125.1|FL065125
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTGGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|211192306|gb|FL065103.1|FL065103
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTGGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|16918829|gb|BM073915.1|BM073915
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|32914236|gb|CF019048.1|CF019048
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|16926343|gb|BM079411.1|BM079411
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|91052589|gb|EB163007.1|EB163007
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|6194643|gb|AW146747.1|AW146747
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTTGTCCCTGCTGATCTTACGGTTGGACAATTCG-G-ATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|93016973|gb|EB642493.1|EB642493
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
EST: gi|211194707|gb|FL065118.1|FL065118
EST:     ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAA                         GTACCTGGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG
genomic: ATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctc ... aactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttgtgtcaaccatagtaagcaataagctgttctgattgtcataactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAGGAAGAGAATCAAGCTCAGTGCTGAGAAAGCTATCTTCATCTTTGTGAAG
                                         tcataac  putative branch site (score: 2)
 ataacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaaaatacttcattaaagcaccattgcacacatcaaagtgttatgtgttgtgtcaaccatagtaagcaataagctgttctgattgtcataactttgcagGTACCTCGTCCCTGCTGATCTTACGGTTGGACAATTCGTGTATGTTGTTAGGAAGAGAATCAAGCTCAGTGCTGAGAAAGCTATCTTCATCTTTGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA