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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccatcttatttgctccattctgaatgctttctttctttggtgtaatcaaggattgttctgtgaagttgcaacgtggtttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTC

Basic information

species Zea mays
transcript GRMZM5G833124_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G833124_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g34650.1 (Oryza sativa), 3'ss of exon 10
--------------gtaccatct-tatttgctccattctgaatgctttctttctttggtgtaatcaaggattg--ttctgtgaagttgcaacgtggtttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTC
               |   ||   ||||||  |         |  |||| ||| || |   |||  || ||||   | ||||||||||  |  |  |||   || ||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| |
gtactatctcgatgatgttattagtatttgtccttagactgttcttttccttcattagcacaatagagcattggcatgtgtgaagttgtgatatattttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCC

upper sequence: GRMZM5G833124_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA17G00580.1 (Glycine max), 3'ss of exon 7
------------------gtaccatcttatttgctccattctgaatgctttctttctttggtgtaatcaaggattgttctgtgaagttgcaacgtg-gtttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTC
                  |    |  || ||     | |||| ||    |    |  ||| ||| || |     |    | | |   || ||  || |||  |   |||   ||||| |||||||| |||||||||||  ||||  ||||||| |||||| |||||||||| || || ||| ||||||||||||| ||||| || || |
gtaaggcctttcttgagagcttgagatttttcagctctttcttaaattatctcctggttgatgtcattatatgatacattctta---tgtaagttgtgttctgtaacagAGGGAGAGATATATTGTGACATATAACCCCTCAAAACACAAGGTTTATGCTGTGCTCAAGGATCAGGCGAAGTCAGATGACATTCTGAAAGCAGCATTCC

upper sequence: GRMZM5G833124_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA07G40210.1 (Glycine max), 3'ss of exon 8
-----------------gtaccatcttatttgctccattctgaatgctttctttctttggtgtaatca-aggat-tgttct-gtg-aagttgcaa---cgtggtttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTC
                 |    |  || ||     | |||| ||       | |  ||| |||  | | | |||   ||||  || ||||||      | |   |||    |||   ||||| |||||||| |||||||||||  ||||  ||||||| |||||  |||||||||| || |||||| ||||||||||||| ||||| || || |
gtaagcctttcttgagagcttgagatttttcagctctttcttaaattaccttctgattgatgttgttatatgatacattcttatgtaagttgtgttctcttaaattgttaacagAGGGAGAGATATATTGTAACATATAACCCCTCAAAACACAAGGTTTATGCGGTGCTCAAGGATCAGGCAAAGTCAGATGACATTCTGAAAGCAGCATTCC

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|91874041|gb|EB403998.1|EB403998
EST:     ATGCGTTTCAAGAACCTGCTTCGTTTCTTGCTATAAAACCTTTGTTCGAG                         GATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
genomic: ATGCGTTTCAAGAACCTGCTTCGTTTCTTGCTATAAAACCTTTGTTCGAGgtaccatctt ... ttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
EST: gi|60356183|gb|DN223156.1|DN223156
EST:     ATGCGTTTCAAGAACCTGCTTCGTTTCTTGCTATAAAACCTTTGTTCGAG                         GATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
genomic: ATGCGTTTCAAGAACCTGCTTCGTTTCTTGCTATAAAACCTTTGTTCGAGgtaccatctt ... ttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
EST: gi|84977310|gb|DW475732.1|DW475732
EST:     ATGCGTTTCAAGAACCTGCTTCGTTTCTTGCTATAAAACCTTTGTTCGAG                         GATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
genomic: ATGCGTTTCAAGAACCTGCTTCGTTTCTTGCTATAAAACCTTTGTTCGAGgtaccatctt ... ttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
EST: gi|32849185|gb|CD988866.1|CD988866
EST:     ATGCGTTTCAAGAACCTGCTTCGTTTCTTGCTATAAAACCTTTGTTCGAG                         GATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
genomic: ATGCGTTTCAAGAACCTGCTTCGTTTCTTGCTATAAAACCTTTGTTCGAGgtaccatctt ... ttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
EST: gi|93281684|gb|EB673948.1|EB673948
EST:     AAACCTTTTTTCGGG                         GATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT
genomic: AAACCTTTGTTCGAGgtaccatctt ... ttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCT

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: 48 (upstream exon), 48 (downstream exon)
Score: 142

GATCAAGATTTGGAGATGCGTTTCAAGAACCTGCTTCGTTTCTTGCTATAAAACCTTTGTTCGAGgtaccatctt ... ttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 307

GATCAAGATTTGGAGATGCGTTTCAAGAACCTGCTTCGTTTCTTGCTATAAAACCTTTGTTCGAGgtaccatctt ... ttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 248

GATCAAGATTTGGAGATGCGTTTCAAGAACCTGCTTCGTTTCTTGCTATAAAACCTTTGTTCGAGgtaccatctt ... ttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 320

GATCAAGATTTGGAGATGCGTTTCAAGAACCTGCTTCGTTTCTTGCTATAAAACCTTTGTTCGAGgtaccatctt ... ttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttggtgtaatcaaggattgttctgtgaagttgcaacgtggtttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTC
          taatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccatcttatttgctccattctgaatgctttctttctttggtgtaatcaaggattgttctgtgaagttgcaacgtggtttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT