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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatataacattgcatataatctgtggttgccacgcccatttttattttattggttttggtacctaaaaggacaattacgtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACCATCATCGGCGGTGGCGACTCTGTCGCTGCTGTCGAGAAGGCTGGGCTGG

Basic information

species Zea mays
transcript GRMZM2G382914_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G382914_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g07260.1 (Oryza sativa), 3'ss of exon 6
gttaatataacattgcatataatctgtggttgccacgcccatttttattttattggttttggtacctaaaaggacaattacgtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACCATCATCGGCGGTGGCGACTCTGTCGCTGCTGTCGAGAAGGCTGGGCTGG
|||| || ||  |||  |   ||| |  | |  |  ||   || ||  |||     |||  ||  |||||    |  |    |||| |||||| |||||||||||| | ||||| ||||| ||||| ||||| | ||| ||||||||||| ||||| ||||| || ||||| |||||||||||||||||||
gttagtacaa--ttgactcacatccgctgatctcctgcattttctttcttt-----tttctgtcgctaaacattc--tcgtctttcatcagGCAATTGCCAAGAAGTTGGCTGATCTTACTACCACAAAGGGCGCCACGACCATCATCGGTGGTGGTGACTCCGTTGCTGCGGTCGAGAAGGCTGGGCTGG
















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|211044128|gb|FL234528.1|FL234528
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCGAGAAGTTTGCAGCTGGCACTGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACN
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|21843580|gb|BQ704161.1|BQ704161
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCGAGAAGTTTGCAGCTGGCACTGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|9824931|gb|BE575028.1|BE575028
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCGAGAAGTTTGCAGCTGGCACTGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|211034531|gb|FL384618.1|FL384618
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAG                         GCGATTGACAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|111990900|gb|EE332336.1|EE332336
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|21987634|gb|BQ779162.1|BQ779162
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCGAGAAGTTTGCAGCTGGCACTGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGGGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|31358967|gb|CD443324.1|CD443324
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCGAGAAGTTTGCAGCTGGCACTGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|21843195|gb|BQ703776.1|BQ703776
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCGAGAAGTTTGCAGCTGGCACTGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|26457504|gb|CA829087.1|CA829087
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCGAGAAGTTTGCAGCTGGCACTGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|22936004|gb|BU572279.1|BU572279
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCGAGAAGTTTGCAGCTGGCACTGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGNGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|32916467|gb|CF021279.1|CF021279
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|211199180|gb|FL385143.1|FL385143
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|31352972|gb|CD437329.1|CD437329
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCGAGAAGTTTGCAGCTGGCACTGAG                         GCGATTGCCCAGAAGCTAGCTGAGCT
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCT
EST: gi|32909025|gb|CF013837.1|CF013837
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|211046002|gb|FL422503.1|FL422503
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCCANAAGTTTGCAGCTGGCACCGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|21843572|gb|BQ704153.1|BQ704153
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCGAGAAGTTTGCAGCTGGCACTGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|32916455|gb|CF021267.1|CF021267
EST:     ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|14243537|gb|BG841279.2|BG841279
EST:     GGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAGCCACGAAGGGTGTCACTACC
genomic: GGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
EST: gi|211233918|gb|FL394222.1|FL394222
EST:     ACGGCCCCATGGGAGTGTTYGAGTTCNAGAAGTTTGCAGCTGGCACTGAG                         GCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC
genomic: ACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACC

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), 49 (downstream exon)
Score: 830

CACCAAAACATTCGACGAAGCATTGGACACCACCAAGACTGTTATTTGGAACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACCATCATCGGCGGTGGCGACTCTGTCGCTGCTGTCGAGAAGGCTGGGCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1053

CACCAAAACATTCGACGAAGCATTGGACACCACCAAGACTGTTATTTGGAACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACCATCATCGGCGGTGGCGACTCTGTCGCTGCTGTCGAGAAGGCTGGGCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 851

CACCAAAACATTCGACGAAGCATTGGACACCACCAAGACTGTTATTTGGAACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACCATCATCGGCGGTGGCGACTCTGTCGCTGCTGTCGAGAAGGCTGGGCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 835

CACCAAAACATTCGACGAAGCATTGGACACCACCAAGACTGTTATTTGGAACGGCCCCATGGGAGTGTTTGAGTTCCAGAAGTTTGCAGCTGGCACCGAGgttaatataa ... gtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACCATCATCGGCGGTGGCGACTCTGTCGCTGCTGTCGAGAAGGCTGGGCTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcccatttttattttattggttttggtacctaaaaggacaattacgtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACCATCATCGGCGGTGGCGACTCTGTCGCTGCTGTCGAGAAGGCTGGGCTGG
                           acctaaa  putative branch site (score: 835)
                                            cgtttcttc  putative PPT
     tttttattttattggt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatataacattgcatataatctgtggttgccacgcccatttttattttattggttttggtacctaaaaggacaattacgtttcttcagGCGATTGCCAAGAAGCTAGCTGAGCTTACAACCACGAAGGGTGTCACTACCATCATCGGCGGTGGCGACTCTGTCGCTGCTGTCGAGAAGGCTGGGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT