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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagcagcgccaacgcggacctcgccgaatttgagtgcgatctggctaatctggggcctggttgccattggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG

Basic information

species Zea mays
transcript GRMZM2G344476_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G344476_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g47120.1 (Oryza sativa), 3'ss of exon 1
gtaaagcagcgccaacgcggacctcgccgaatttgagtgcgatc-tggctaatctggggcctggttgccattggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG
||||||||||||       || | ||||||||||  | ||| || ||||||||| | ||  |||||||||||||||||||||||| || ||||| |||||||||||||||||||||||||||||  | ||||| |||||||| ||||| || ||||||| ||| |||  |||||
gtaaagcagcgc------agagcccgccgaatttaggagcgctcctggctaatccgaggggtggttgccattggtgtgcagTGACGGAGTTCCTCGGCCAGGTGCCCCTCCTGCAGTGCCTCCCCAGCTCCTCCATCCGCAGGATCGCCGACGCCGTCCTGGTGAAGCGCTACG
















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|50337659|gb|CO532785.1|CO532785
EST:     ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAG                         TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
genomic: ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
EST: gi|148956464|gb|EC902291.2|EC902291
EST:     ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAG                         TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
genomic: ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
EST: gi|74238643|gb|DT646557.1|DT646557
EST:     ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAG                         TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
genomic: ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
EST: gi|211119071|gb|FL021982.1|FL021982
EST:     ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAG                         TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
genomic: ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
EST: gi|149104205|gb|EE289638.2|EE289638
EST:     ACCCCTGCTCGCCGTTCCTGCAGCCGCACAGGCGATGGATCATGAAGAAG                         TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
genomic: ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
EST: gi|148936448|gb|EC880552.2|EC880552
EST:     ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAG                         TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
genomic: ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
EST: gi|149112589|gb|EE191373.2|EE191373
EST:     ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAG                         TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCCCCCGGGTTCCT
genomic: ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
EST: gi|91872284|gb|EB402241.1|EB402241
EST:     ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAG                         TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
genomic: ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
EST: gi|71315516|gb|DR794364.1|DR794364
EST:     ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAG                         TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
genomic: ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
EST: gi|50331303|gb|CO526429.1|CO526429
EST:     ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAG                         TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
genomic: ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
EST: gi|148958992|gb|EE010517.2|EE010517
EST:     ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAG                         TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
genomic: ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
EST: gi|148944150|gb|EC889238.2|EC889238
EST:     ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAG                         TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
genomic: ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
EST: gi|4730512|gb|AI649678.1|AI649678
EST:     ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAG                         TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
genomic: ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
EST: gi|71315960|gb|DR794668.1|DR794668
EST:     ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAG                         TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
genomic: ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
EST: gi|91875931|gb|EB405888.1|EB405888
EST:     ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAG                         TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT
genomic: ACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCT

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: 20 (upstream exon), 48 (downstream exon)
Score: 18

TCGCGTCCTCCGCCCTCAACCGTAGCCACCTCGCTGCCCCTGCCGCCGACACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 41

TCGCGTCCTCCGCCCTCAACCGTAGCCACCTCGCTGCCCCTGCCGCCGACACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG


Block sizes: 27 (upstream exon), 45 (downstream exon)
Score: 43

TCGCGTCCTCCGCCCTCAACCGTAGCCACCTCGCTGCCCCTGCCGCCGACACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG


Block sizes: 26 (upstream exon), 49 (downstream exon)
Score: 32

TCGCGTCCTCCGCCCTCAACCGTAGCCACCTCGCTGCCCCTGCCGCCGACACCCCTGCTCGCCGTTGCTGCAGCCGCACAGGCGATGGATCATGAAGAAGgtaaagcagc ... tggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccgaatttgagtgcgatctggctaatctggggcctggttgccattggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG
                    ggctaat  putative branch site (score: 32)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagcagcgccaacgcggacctcgccgaatttgagtgcgatctggctaatctggggcctggttgccattggtgtgcagTGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG

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