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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatcctgtgtagtactgtagcaaaatttctgctttataaactgtcacttggctctcgagtagatcattctaaccattgccaatttgatctgttttgtagATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGTGGAAGAAGCATGCTGCAAAAGTTAGGCCTTCAGAACTATGAGAAGAACT

Basic information

species Zea mays
transcript GRMZM2G089507_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089507_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g33220.1 (Oryza sativa), 3'ss of exon 3
--gtatcctgtgtagtactgtagcaaaatttctgctttataaactgtcacttggctctcgagtagatcattctaaccattgccaatttgatctgttttgtagATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGTGGAAGAAGCATGCTGCAAAAGTTAGGCCTTCAGAACTATGAGAAGAACT
  ||     |  ||| | |   |    |||  | || |      |  |  |    |    |  || |  |  |     ||||| |    |||| ||||||||||   ||| |||||||| ||||||| ||||| ||||| ||||||||| ||||| ||||  ||| || || | ||||| |||||||||||||||||||| |
ctgtcagtggattaggatttagggcccattggtactatcctttttagcgataaatttgatatcag-ttgtaattctttttgcctaca-aatctattttgtagATTGGTCAGAAATTTTCGCAGCCACCGAGTGAAGATATATACTATTCCCGTGGGAGAAATATGTTGAAACAATTAGGGCTTCAGAACTATGAGAAGAATT
















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|148947688|gb|EC893169.2|EC893169
EST:     CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATG                         ATCTCTCAAAAATTTTCACAGCCCCAGAGTGGAGATACATACTATTCTCGT
genomic: CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATGgtaagaatct ... tgttttgtagATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGT
EST: gi|149073933|gb|EE162260.2|EE162260
EST:     CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATG                         ATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGT
genomic: CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATGgtaagaatct ... tgttttgtagATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGT
EST: gi|4612872|gb|AI603711.1|AI603711
EST:     CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATG                         ATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGT
genomic: CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATGgtaagaatct ... tgttttgtagATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGT
EST: gi|149111703|gb|EE190848.2|EE190848
EST:     CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATG                         ATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGT
genomic: CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATGgtaagaatct ... tgttttgtagATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGT
EST: gi|149073934|gb|EE162261.2|EE162261
EST:     CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATG                         ATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGT
genomic: CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATGgtaagaatct ... tgttttgtagATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGT
EST: gi|148947689|gb|EC893170.2|EC893170
EST:     CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATG                         ATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGT
genomic: CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATGgtaagaatct ... tgttttgtagATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGT
EST: gi|20507320|gb|BQ279578.1|BQ279578
EST:     CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGGTTTTTCATG                         ATCTCTCAAAAATTTTCACAGC
genomic: CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATGgtaagaatct ... tgttttgtagATCTCTCAAAAATTTTCACAGC
EST: gi|149111704|gb|EE190849.2|EE190849
EST:     CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATG                         ATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGT
genomic: CAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATGgtaagaatct ... tgttttgtagATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGT

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), 49 (downstream exon)
Score: 82

TCTATTCTCCATCGTGAGTGGAATGGGGACCCCAAATCCAGTAGCTAATGCAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATGgtaagaatct ... tgttttgtagATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGTGGAAGAAGCATGCTGCAAAAGTTAGGCCTTCAGAACTATGAGAAGAACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 97

TCTATTCTCCATCGTGAGTGGAATGGGGACCCCAAATCCAGTAGCTAATGCAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATGgtaagaatct ... tgttttgtagATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGTGGAAGAAGCATGCTGCAAAAGTTAGGCCTTCAGAACTATGAGAAGAACT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 34

TCTATTCTCCATCGTGAGTGGAATGGGGACCCCAAATCCAGTAGCTAATGCAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATGgtaagaatct ... tgttttgtagATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGTGGAAGAAGCATGCTGCAAAAGTTAGGCCTTCAGAACTATGAGAAGAACT


Block sizes: 46 (upstream exon), 39 (downstream exon)
Score: 60

TCTATTCTCCATCGTGAGTGGAATGGGGACCCCAAATCCAGTAGCTAATGCAATTACAACTGGTGTTGGTTTTGCTGTATTTCAAGGTGGTTTTTTCATGgtaagaatct ... tgttttgtagATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGTGGAAGAAGCATGCTGCAAAAGTTAGGCCTTCAGAACTATGAGAAGAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttggctctcgagtagatcattctaaccattgccaatttgatctgttttgtagATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGTGGAAGAAGCATGCTGCAAAAGTTAGGCCTTCAGAACTATGAGAAGAACT
                                           tctgtttt  CT-rich tract
                                    aatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctgtgtagtactgtagcaaaatttctgctttataaactgtcacttggctctcgagtagatcattctaaccattgccaatttgatctgttttgtagATCTCTCAAAAATTTTCACAGCCACAGAGTGGAGATACATACTATTCTCGTGGAAGAAGCATGCTGCAAAAGTTAGGCCTTCAGAACTATGAGAAGAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- -tcctgtg
- - - - - - - -ctgtagc
- - - - - - - - - - - - - -ttctgct
- - - - - - - - - - - - - - - - - - - - -ctgtcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattgc