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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagaaagtaattcctccttttcatggtgccagagatgacacattcctttttgcaagtttttagttcacatgtaaaactcttgctattttaataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC

Basic information

species Zea mays
transcript GRMZM2G152775_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152775_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g53060.1 (Oryza sativa), 3'ss of exon 2
-atagaaagtaat--tcctccttttcatggtgccagagatgacacattcctttttgcaagtttttagttcacatgtaaaactcttgctattttaataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC
  |||    || |  ||  | | |   |  |  |||  | | ||  ||||      | |||  |   ||||||||||||  | |   | | |   |  |||||||||||||||||||||| ||||| ||||||||||||||||| ||||||||||||||
tgtagttgttagtagtcggcttctaattattatcagctaaggcat-ttccaagagtccagtagt--attcacatgtaaatatttgtttctctctgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC

upper sequence: GRMZM2G152775_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g04800.1 (Oryza sativa), 3'ss of exon 2
atagaaagtaattcctccttttcatggtgccagagatg-acacattcctttttgcaagtttt----tagttcacatgtaaaactcttgctattttaataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC
 |      || ||  |  |  ||   || | |   | | |   |||      | ||   |||    ||||||||  |||  |   ||   |||    |  |||||||||| || ||||||||||||||||| |||||||||||||| ||||||||||||||
-tttttcatagttgttaatagtc-cagtactaagtaagtaagtattatcagatacagcatttccaatagttcactagtattatatttctcatt---gtctcacagGCTGCCGACACACAAGTCATTTCGGAATATGTACGCTATTTTCTCCACCAACACAC
















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|211427386|gb|FK988649.1|FK988649
EST:     CAAGATTACTNCA-CTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCCAC-A
genomic: CAAGATTACT-CAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTgtaagtgcca ... aataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCC-ACCA
EST: gi|89252178|gb|DY623964.1|DY623964
EST:     ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAC
genomic: ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTgtaagtgcca ... aataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA
EST: gi|211424798|gb|FK988647.1|FK988647
EST:     ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTYCATTTCGGATTATGTACGCTATTTCCTCYACCA
genomic: ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTgtaagtgcca ... aataccacagGCTGCTGATACACAAGT-CATTTCGGATTATGTACGCTATTTCCTCCACCA
EST: gi|211419584|gb|FK988617.1|FK988617
EST:     ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA
genomic: ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTgtaagtgcca ... aataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA
EST: gi|211422177|gb|FK988623.1|FK988623
EST:     ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA
genomic: ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTgtaagtgcca ... aataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA
EST: gi|211422175|gb|FK988621.1|FK988621
EST:     ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA
genomic: ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTgtaagtgcca ... aataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA
EST: gi|148946911|gb|EC892193.2|EC892193
EST:     ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA
genomic: ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTgtaagtgcca ... aataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA
EST: gi|76925303|gb|DV170371.1|DV170371
EST:     CAAGATTTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT                         GCTGCTGATACCCAAGTCATTTCGGATTATGTACGCTATTTCCTCC-CCAA
genomic: CAAGATT-ACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTgtaagtgcca ... aataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA
EST: gi|211419574|gb|FK988607.1|FK988607
EST:     ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA
genomic: ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTgtaagtgcca ... aataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA
EST: gi|211424796|gb|FK988645.1|FK988645
EST:     ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA
genomic: ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTgtaagtgcca ... aataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA
EST: gi|211424797|gb|FK988646.1|FK988646
EST:     ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT                         GCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA
genomic: ACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTgtaagtgcca ... aataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAA

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), 48 (downstream exon)
Score: 461

GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTgtaagtgcca ... aataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 409

GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTgtaagtgcca ... aataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 355

GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTgtaagtgcca ... aataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 391

GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTgtaagtgcca ... aataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttttgcaagtttttagttcacatgtaaaactcttgctattttaataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC
                                         ttttaat  putative branch site (score: 391)
                                   ttgctattttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagaaagtaattcctccttttcatggtgccagagatgacacattcctttttgcaagtttttagttcacatgtaaaactcttgctattttaataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC

- -gaaagtaa
- - - - - - - - - - - - tggtgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttgc