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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatttttactagtgcattgtttagcttttgcagattgttttaggcttttagcttctaatgtatgatacctattgctcacttttttttttttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCACGAATCCTTCAACGCCACTTCAAAGGAAAGCCATATTATGTTGATATCA

Basic information

species Zea mays
transcript GRMZM2G098569_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 3
--ttcatttttactagtgcat-tgtttagcttttgcagattgttttaggcttttagcttctaatgtatgataccta-ttgctcacttttttttttttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCACGAATCCTTCAACGCCACTTCAAAGGAAAGCCATATTATGTTGATATCA
  |||| |  |  ||  |  | || | || ||  ||| | ||||   |  ||      | | |  ||| | ||  | ||  |   |||  || |||||||||||||||| |||||||| ||||||||||| |||||||||||||| ||||| |||||||| ||||||||||| || ||||||||||  |||||||||||| |||
ttttcaatccttgtaaggagtgtgatcagatta-gcacaatgtt---gaattgctatctgttacctataaaactaaatttgtgtatttcattgttttgcaatagGTTGGGCTCATTGCTGTAAATGATGGTATTATCCTTCGCAACCATATTTCACGAATTCTTCAACGCCATTTTAAAGGAAAGCTGTATTATGTTGATCTCA
















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|71306846|gb|DR789579.1|DR789579
EST:     ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG                         GTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
genomic: ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttagatcag ... tttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
EST: gi|211448759|gb|FL324438.1|FL324438
EST:     ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG                         GTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
genomic: ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttagatcag ... tttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
EST: gi|60352104|gb|DN219077.1|DN219077
EST:     ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG                         GTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAAACATATCTCA
genomic: ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttagatcag ... tttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
EST: gi|148951738|gb|EC897493.2|EC897493
EST:     ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG                         GTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
genomic: ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttagatcag ... tttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
EST: gi|149100779|gb|EE186873.2|EE186873
EST:     ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG                         GTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
genomic: ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttagatcag ... tttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
EST: gi|148950117|gb|EC895653.2|EC895653
EST:     ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG                         GTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
genomic: ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttagatcag ... tttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
EST: gi|71310911|gb|DR791758.1|DR791758
EST:     ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG                         GTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
genomic: ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttagatcag ... tttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
EST: gi|211504975|gb|FL314285.1|FL314285
EST:     ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG                         GTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
genomic: ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttagatcag ... tttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
EST: gi|148964886|gb|EE015748.2|EE015748
EST:     ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG                         GTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
genomic: ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttagatcag ... tttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
EST: gi|78117582|gb|DV535969.1|DV535969
EST:     ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG                         GTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA
genomic: ACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttagatcag ... tttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCA

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: 49 (upstream exon), 45 (downstream exon)
Score: 195

CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttagatcag ... tttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCACGAATCCTTCAACGCCACTTCAAAGGAAAGCCATATTATGTTGATATCA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 858

CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttagatcag ... tttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCACGAATCCTTCAACGCCACTTCAAAGGAAAGCCATATTATGTTGATATCA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 707

CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttagatcag ... tttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCACGAATCCTTCAACGCCACTTCAAAGGAAAGCCATATTATGTTGATATCA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 270

CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttagatcag ... tttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCACGAATCCTTCAACGCCACTTCAAAGGAAAGCCATATTATGTTGATATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttttagcttctaatgtatgatacctattgctcacttttttttttttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCACGAATCCTTCAACGCCACTTCAAAGGAAAGCCATATTATGTTGATATCA
                             tgctcac  putative branch site (score: 270)
                        cctattgctcactttt  CT-rich tract
                                    ttttttttttttgcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcatttttactagtgcattgtttagcttttgcagattgttttaggcttttagcttctaatgtatgatacctattgctcacttttttttttttgcaatagGTTGGTCTCATTGCAGTAAATGATGGGATTATCCTTCGCAATCATATCTCACGAATCCTTCAACGCCACTTCAAAGGAAAGCCATATTATGTTGATATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
ttcattt
- - - - - - -gtgcatt
- - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - -agcttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtatg