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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaacctgtcgcgtatcttatgcctgaaataattgatggtttgtaagttagaataggaccactcatttttccgtataacaccttcaagctttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAGAGAGAGCGCCATGTGATCGTCCGGAAGGCTTGATGTGGAGAGTCCAGTC

Basic information

species Zea mays
transcript GRMZM2G450055_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G450055_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 16
gtacgaacctgtcgcgtatcttatgcctgaaataattgatggtttgtaagttagaataggaccactcatttttccgtataacaccttcaagctttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAGAGAGAGCGCCATGTGATCGTCCGGAAGGCTTGATGTGGAGAGTCCAGTC
             | | | | | |      | || ||| |  ||  | | ||    ||| | ||     |||| | |||   ||| |   |||  | |||||||| ||||||| |||||||| ||||| ||||| || || |||||||||||||||||||||||||| || ||||||||||||||| ||| |  ||  ||| 
-----------gtgaggaacctgt---catactatttgctatttaattaattgatttagtatca-----tttttcttatgctaccattcggct--gcttcagGTGCGAAGAGCCCTTCTGATCATGCACCAAAGGGATGAAGTGGAGTACAAGAGAGAGCGCCATGTCATTGTCCGGAAGGCTTGAGGTGAACTGTGGAGTA
















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|5468568|gb|AI834359.1|AI834359
EST:     AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATT                         GTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
EST: gi|211022394|gb|FL169361.1|FL169361
EST:     AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATT                         GTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
EST: gi|78112948|gb|DV531342.1|DV531342
EST:     AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATT                         GTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
EST: gi|78090564|gb|DV518938.1|DV518938
EST:     AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATT                         GTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
EST: gi|67013180|gb|CO441929.1|CO441929
EST:     AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATT                         GTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
EST: gi|33092334|gb|CF052328.1|CF052328
EST:     AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATT                         GTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGT
genomic: AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGT
EST: gi|71437031|gb|DR818081.1|DR818081
EST:     AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATT                         GTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
EST: gi|211022393|gb|FL169360.1|FL169360
EST:     AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATT                         GTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
EST: gi|89763462|gb|DY690644.1|DY690644
EST:     AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATT                         GTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
EST: gi|21759869|gb|BQ635410.1|BQ635410
EST:     AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATT                         GTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
EST: gi|16925423|gb|BM078491.1|BM078491
EST:     AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATT                         GTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
EST: gi|78024159|gb|DV492546.1|DV492546
EST:     AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATT                         GTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
EST: gi|22472717|gb|BU037197.1|BU037197
EST:     AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGTATCCATT                         GTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
EST: gi|211197837|gb|FL437951.1|FL437951
EST:     GCGACGGCTGATTGATGGACTAAACAGGGATGGGAATGAACGAATCCATT                         GTGAGAAGAGCTCTTCTGATTATGCATC-AAGAGACGAGGTGGGAGTACAA
genomic: GCGACGGCTGATTGATGGACTAAACA-GGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGT-GGAGTACAA
EST: gi|16918329|gb|BM073698.1|BM073698
EST:     AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATT                         GTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAG

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: 48 (upstream exon), 46 (downstream exon)
Score: 110

AGCGGAAGCACAGATAAAGCGAAGAATGGGCATTGGAAGCCACATATCTGAGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAGAGAGAGCGCCATGTGATCGTCCGGAAGGCTTGATGTGGAGAGTCCAGTC


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 27

AGCGGAAGCACAGATAAAGCGAAGAATGGGCATTGGAAGCCACATATCTGAGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAGAGAGAGCGCCATGTGATCGTCCGGAAGGCTTGATGTGGAGAGTCCAGTC


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 31

AGCGGAAGCACAGATAAAGCGAAGAATGGGCATTGGAAGCCACATATCTGAGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAGAGAGAGCGCCATGTGATCGTCCGGAAGGCTTGATGTGGAGAGTCCAGTC


Block sizes: 46 (upstream exon), 40 (downstream exon)
Score: 11

AGCGGAAGCACAGATAAAGCGAAGAATGGGCATTGGAAGCCACATATCTGAGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCATTgtacgaacct ... tttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAGAGAGAGCGCCATGTGATCGTCCGGAAGGCTTGATGTGGAGAGTCCAGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttagaataggaccactcatttttccgtataacaccttcaagctttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAGAGAGAGCGCCATGTGATCGTCCGGAAGGCTTGATGTGGAGAGTCCAGTC
                            gtataac  putative branch site (score: 11)
                                            ctttgtttc  putative PPT
                  tcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgaacctgtcgcgtatcttatgcctgaaataattgatggtttgtaagttagaataggaccactcatttttccgtataacaccttcaagctttgtttcagGTGAGAAGAGCTCTTCTGATTATGCATCAAAGAGACGAGGTGGAGTACAAGAGAGAGCGCCATGTGATCGTCCGGAAGGCTTGATGTGGAGAGTCCAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA