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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtaaaattgctagtccctttatattgcttcatattattgatcaatttggtgcacaatcttagtgtttgcatcatattatgttcctatctaaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG

Basic information

species Zea mays
transcript GRMZM2G104769_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104769_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g02140.3 (Oryza sativa), 3'ss of exon 2
gtgtgtaaaattgctagtccct------ttatattgcttcatattattgatcaatttggtgcacaatcttagtgtttgcatcatattatgttcctatctaaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG
|| |||| || |  || | |||      || | ||||| || |||   || ||||| | | |||| |  |  || || || |||| | ||    | |     | |||||||||||  ||| | |||||||||||| ||||||||||| |||||||||||||| |||||||||
gtctgtataactattatttcctcttctttttttttgctgcacattgg-gagcaatt-gattcacatttatgttgcttacaccatactttgccaatctgagttttgcagTGAGTGGGTTAGGGCTGAGGAAGATTGTAGAACAGCTATTCAGCTTGACAGCCACTCTGTTAAG
















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|76913822|gb|DV165266.1|DV165266
EST:     AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAA                         TGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
genomic: AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
EST: gi|211321471|gb|FL171489.1|FL171489
EST:     ATGTTGCAGTATATTNGGACCAACCGAGCACTTTGCTATAGGAAGCGGAA                         TGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
genomic: ATGTTGCAGTATATT-GGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
EST: gi|211321469|gb|FL171487.1|FL171487
EST:     AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAA                         TGAGTGCACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
genomic: AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
EST: gi|211321468|gb|FL171486.1|FL171486
EST:     AATGTTGCAGTATAT-GGACCAACCGAGCACTTTGCTATAGGAAGCGGAA                         TGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
genomic: AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
EST: gi|211321470|gb|FL171488.1|FL171488
EST:     AATGTTGCAGTATAT-GGASCAACCGAGCACTTTGCTATAGGAAGCGGAA                         TGAGTGGACYAGAGTTGAGGAAGATTTGCWGAACAGCTATCCAGCTTGACA
genomic: AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATT-GCAGAACAGCTATCCAGCTTGACA
EST: gi|94476727|gb|EB705685.1|EB705685
EST:     AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAA                         TGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
genomic: AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
EST: gi|211196887|gb|FL171483.1|FL171483
EST:     AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAA                         TGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
genomic: AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
EST: gi|61119637|gb|DN560598.1|DN560598
EST:     AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAA                         TGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
genomic: AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
EST: gi|211321467|gb|FL171485.1|FL171485
EST:     AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAA                         TGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
genomic: AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
EST: gi|211321466|gb|FL171484.1|FL171484
EST:     AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAA                         TGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
genomic: AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
EST: gi|149106376|gb|EE292096.2|EE292096
EST:     AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAA                         TGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
genomic: AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
EST: gi|91054321|gb|EB164739.1|EB164739
EST:     AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAA                         TGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG
genomic: AATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAG

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: 46 (upstream exon), 44 (downstream exon)
Score: 45

GCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

GCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

GCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG


Block sizes: 46 (upstream exon), 40 (downstream exon)
Score: 48

GCCATAACTCTTTGCCCAAATGTTGCAGTATATTGGACCAACCGAGCACTTTGCTATAGGAAGCGGAAgtgtgtaaaa ... taaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttggtgcacaatcttagtgtttgcatcatattatgttcctatctaaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG
                                          atctaaa  putative branch site (score: 48)
                                     ttcctatct  CT-rich tract
                          atcatattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtaaaattgctagtccctttatattgcttcatattattgatcaatttggtgcacaatcttagtgtttgcatcatattatgttcctatctaaatggcagTGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA