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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggcctcaattttatggctcgtttttgctatactaatacatctggtcaataacttttatgttttagttcacaactcctaaaaacgctctcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG

Basic information

species Zea mays
transcript GRMZM2G128995_T05
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128995_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 4
-tttggcctcaattttatggctcgtttttgctatactaatacatctggtcaataacttttatgttttagttcacaactcctaaaaacgctctct-tccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG
 |          |||| | ||      ||   |  |  | |   ||      | || | |    ||||   ||      || ||   | | | |  |  |||||||||| | ||||||| ||||||||||||||||||||||||||||||||||| ||||||| ||| ||
atccacgtctccttttttagcattgagttatcacgc--acaacactacagcgtgacctgttgaatttacaacagctgagctgaatgtgttttttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG
















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|67018576|gb|CO447325.1|CO447325
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|211478907|gb|FL382317.1|FL382317
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTYCGAGCATCAGAATATAATAATGT
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGT
EST: gi|211045930|gb|FL419466.1|FL419466
EST:     GTCGGCAGCATACAGTCACAGGTTGCCAGAGATCGAGGCATGACATGAAG                         GTTCGAGCATCAGAATATAATAATGTAAGGAGCCAGCTTAGTGGGATCAAC
genomic: GTCGGCAGCATACAGTCACAGGTTGCCA-AGATCGAGG-ATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|211327966|gb|FL399630.1|FL399630
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGT
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGT
EST: gi|211065673|gb|FL393994.1|FL393994
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCAGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|71427970|gb|DR809020.1|DR809020
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|211413494|gb|FL407160.1|FL407160
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|211452191|gb|FL398498.1|FL398498
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|149010225|gb|EE042044.2|EE042044
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|19351525|gb|BM896057.1|BM896057
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCAGAATATAATAATGCAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|31348626|gb|CD432983.1|CD432983
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCAGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|149000734|gb|EE037952.2|EE037952
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|148954149|gb|EC899548.2|EC899548
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|67013699|gb|CO442448.1|CO442448
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|22491457|gb|BU051380.1|BU051380
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCAGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|211319940|gb|FL427662.1|FL427662
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCNAGCTTAGTGCGATCAA
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCC-AGCTTAGTGCGATCAA
EST: gi|211452273|gb|FL403779.1|FL403779
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GNTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTT
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTT
EST: gi|87153287|gb|DY398076.1|DY398076
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCAGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|6095541|gb|AW120208.1|AW120208
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCAGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|148968978|gb|EE019672.2|EE019672
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|148963815|gb|EE014912.2|EE014912
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|211288089|gb|FL387847.1|FL387847
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCA
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCA
EST: gi|31363830|gb|CD448185.1|CD448185
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCCAGCATCACAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|211169417|gb|FL381630.1|FL381630
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCAAAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCA-C
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|149098811|gb|EE184822.2|EE184822
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|78076482|gb|DV504916.1|DV504916
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCA
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCA
EST: gi|211532950|gb|FL381081.1|FL381081
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|60358961|gb|DN225934.1|DN225934
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|211017234|gb|FL404253.1|FL404253
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCAGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
EST: gi|211057980|gb|FL426570.1|FL426570
EST:     TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAG                         GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC
genomic: TCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAAC

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: 137

GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCCCCTCTCAAGGAGATCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCCCCTCTCAAGGAGATCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCCCCTCTCAAGGAGATCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 292

GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCCCCTCTCAAGGAGATCGTCGGCAGCATACAGTCACAGGTTGCCAAGATCGAGGATGACATGAAGgtttgtttgc ... tcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcaataacttttatgttttagttcacaactcctaaaaacgctctcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG
                               tcctaaa  putative branch site (score: 292)
                                        cgctctcttcccc  putative PPT
     ataacttttatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggcctcaattttatggctcgtttttgctatactaatacatctggtcaataacttttatgttttagttcacaactcctaaaaacgctctcttccccagGTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG