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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagtttggctttggatttactgacttgagcaatgttcatttgcttttcttggggtagccgttttatatgtttctctaaagaatacatttggttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGATCTTAGAAGAACGAACTCAATGCAGTGGTAGATTGGAGCCAAGCTCAGTC

Basic information

species Zea mays
transcript GRMZM5G858197_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G858197_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g64730.1 (Oryza sativa), 3'ss of exon 3
cagtttggctttggatttactgacttgagcaatgttcatttgctt-ttcttggggtagccgttttatatgtttctctaaagaa-tacatttggttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGATCTTAGAAGAACGAACTCAATGCAGTGGTAGATTGGAGCCAAGCTCAGTC
 |            || |  ||         ||| |||||  ||  ||| |  |||   | |     ||| || ||| ||||| |   |||  || |||||||||  ||||  |||    ||||||||  | |||||||   || || |||||||||||||||| ||||| ||| |||||||||   |||||||||||||| 
aaaaaaaaaaaaaaatcttttgcaaatctatatgctcattaactcattcattaggt--tcatcgatcatgcttatctgaagaaatctgtttactttatgcagCTCAAGGAAATGGTTGTTCCAGTCATCATTAGGAAAACGTCAGCACGAGATCTTAGAAGAACAAACTCGATGGAGTGGTAGACGTGAGCCAAGCTCAGTT
















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|211278317|gb|FL464695.1|FL464695
EST:     GAAGAGCGGCACCAGAAGCGGCTTAAAGAG                         CTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
genomic: GAAGAGCGGCACCAGAAGCGGCTTAAAGAGgtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
EST: gi|154130372|gb|EC872158.2|EC872158
EST:     GAAGAGCGGCACCAGAAGCGGCTTAAAGAG                         CTCTTGGAACGGGTGACGCCAGTCATTTTGAGGAAAAAACCATCAGGAGAT
genomic: GAAGAGCGGCACCAGAAGCGGCTTAAAGAGgtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
EST: gi|211224501|gb|FL435966.1|FL435966
EST:     GAAGAGCGGCACCAGAAGCGGCTTAAAGAGG                         CTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGA
genomic: GAAGAGCGGCACCAGAAGCGGCTTAAAGA-Ggtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGA
EST: gi|37374163|gb|CF623418.1|CF623418
EST:     GAAGAGCGGCACCAGAAGCGGCTTAAAGAG                         CTCTTGGAACGGGTGACCCCAGTCATTTTGAGGAAAAAACCATCAGGAGAT
genomic: GAAGAGCGGCACCAGAAGCGGCTTAAAGAGgtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
EST: gi|211132670|gb|FL468288.1|FL468288
EST:     GAAGAGCGGCACCAGAAGCGGCTTAAARAG                         CTCTTGGAACGGGTGACGCCAGTCATTYTGAGGAAAAAACCATCAGGAGAT
genomic: GAAGAGCGGCACCAGAAGCGGCTTAAAGAGgtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
EST: gi|149112568|gb|EE191364.2|EE191364
EST:     GAAGAGCGGCACCAGAAGCGGCTTAAAGAG                         CTCTTGGAACGGGTGACGCCAGTCATTTTGAGGAAAAAACCATCAGGAGAT
genomic: GAAGAGCGGCACCAGAAGCGGCTTAAAGAGgtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
EST: gi|78544178|gb|DV621676.1|DV621676
EST:     GAAGAGCGGCACCAGAAGCGGCTTAAAGAG                         CTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
genomic: GAAGAGCGGCACCAGAAGCGGCTTAAAGAGgtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
EST: gi|40302941|gb|CK347328.1|CK347328
EST:     GGAAGAGCGGCACCAGAAGCGGCTTAAAGAG                         CTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
genomic: GGAAGAGCGGCACCAGAAGCGGCTTAAAGAGgtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
EST: gi|37374161|gb|CF623417.1|CF623417
EST:     GAAGAGCGGCACCAGAAGCGGCTTAAAGAG                         CTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
genomic: GAAGAGCGGCACCAGAAGCGGCTTAAAGAGgtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
EST: gi|211278318|gb|FL464696.1|FL464696
EST:     GAAGAGCGGCACCAGAAGCGGCTTAAAGAG                         CTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
genomic: GAAGAGCGGCACCAGAAGCGGCTTAAAGAGgtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
EST: gi|40303388|gb|CK347775.1|CK347775
EST:     GAAGAGCGGCACCAGAAGCGGCTTAAAGAG                         CTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
genomic: GAAGAGCGGCACCAGAAGCGGCTTAAAGAGgtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
EST: gi|19769681|gb|BQ034402.1|BQ034402
EST:     GAAGAGCGGCACCAGAAGCGGCTTAAAGAG                         CTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT
genomic: GAAGAGCGGCACCAGAAGCGGCTTAAAGAGgtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGAT

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: 36 (upstream exon), 49 (downstream exon)
Score: 77

GAAGAGCGGCACCAGAAGCGGCTTAAAGAGgtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGATCTTAGAAGAACGAACTCAATGCAGTGGTAGATTGGAGCCAAGCTCAGTC


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 94

GAAGAGCGGCACCAGAAGCGGCTTAAAGAGgtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGATCTTAGAAGAACGAACTCAATGCAGTGGTAGATTGGAGCCAAGCTCAGTC


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 89

GAAGAGCGGCACCAGAAGCGGCTTAAAGAGgtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGATCTTAGAAGAACGAACTCAATGCAGTGGTAGATTGGAGCCAAGCTCAGTC


Block sizes: 30 (upstream exon), 49 (downstream exon)
Score: 176

GAAGAGCGGCACCAGAAGCGGCTTAAAGAGgtaacttcct ... gttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGATCTTAGAAGAACGAACTCAATGCAGTGGTAGATTGGAGCCAAGCTCAGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttggggtagccgttttatatgtttctctaaagaatacatttggttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGATCTTAGAAGAACGAACTCAATGCAGTGGTAGATTGGAGCCAAGCTCAGTC
               ttttatatgtttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagtttggctttggatttactgacttgagcaatgttcatttgcttttcttggggtagccgttttatatgtttctctaaagaatacatttggttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGATCTTAGAAGAACGAACTCAATGCAGTGGTAGATTGGAGCCAAGCTCAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA