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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttcttctttttgactaccattttttttagtttcttaggcagtatcaaatttggataaccatataagaattttcagctggtttttaattttatatgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG

Basic information

species Zea mays
transcript GRMZM2G018697_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 6
gttttcttctttttgactaccattttttttagtttcttaggcagtatcaaatttggataaccatataagaattttcagctggtttttaat-tttatatga-----tgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG
|||||    ||| ||| |            | | | | |  | | || ||||||  || | |||   || ||       || | |||||| |||||||       |   ||||||| || |||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||
gtttttcagtttctgattga-gcggcacccattctttgaaactggattaaattta-atgaacattccaggatcgatgtatgatctttaatctttatattgcattttagtagGTGGTCAACAGATATATTGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTCTGTTCATTGATGAG

upper sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 6
gttttcttctttttgac-taccattttttttagtttcttaggcagtatcaaatttggataaccatataagaattttcagctggtttttaattt------tatatgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG
|| |||   |||   |  || ||    |  |  |||   | |  | | || ||||  |||| ||| | || |||  ||  || | |||||  |      | |||| ||  ||||||| || |||||||| |||||||||||||| |||||||||||||||||| |||||||||| |||
gtattcaaatttcccatgtagcagcactgctgcttttaaaagtgg-accacattta-ataaacatgtcaggattggcatatgatctttaacatctatactgtatgttgctagGTGGTTAACAGATATATTGATGAAGGAATTGCTGAGCTTGTACCTGGTGTTCTGTTCATTGACGAG

upper sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 7
lower sequence: EFJ27201 (Selaginella moellendorffii), 3'ss of exon 6
gttttcttctttttgactaccattttttttagtttcttaggcagtatcaaatttggataaccatataagaattttcagctggtttttaattttatatgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG
              |    ||  | ||  |    |||   |   |    | |||  ||   | || | || | |      | | |||            || |||||||| ||||| ||||| ||| ||||| | || |||||||||||||||||  | || ||||| |||
--------------gttagccggtgttcgtcagctctcctgttttgaggattttctattgtc-tagaggattatgtgtgggatctttg-----------tggcagGTGGTTAATAGGTATATTGATCAAGGAGTGGCGGAGCTTGTACCTGGTGTCCTATTTATTGACGAG

upper sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 7
lower sequence: EFJ33466 (Selaginella moellendorffii), 3'ss of exon 6
gttttcttctttttgactaccattttttttagtttcttaggcagtatcaaatttggataaccatataagaattttcagctggtttttaattttatatgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG
            ||  |  ||    ||  |    |||    | || || |   |     |   | |||    ||     |||  | |         |  || |||||||| ||||| ||||| ||| ||||| | || |||||||||||||||||  | || ||||| |||
-----------gttagcagccggcgttcgtcagctctc---ctgtttcgaggattttctattgtctaaaggattatgtgtggcatgt---------ttgtggcagGTGGTTAATAGGTATATTGATCAAGGAGTGGCGGAGCTTGTACCTGGTGTCCTATTTATTGACGAG

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|60340836|gb|DN207809.1|DN207809
EST:     AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAG                         GTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTT
genomic: AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttct ... atgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTT
EST: gi|22490622|gb|BU050545.1|BU050545
EST:     AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAG                         GTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTT
genomic: AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttct ... atgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTT
EST: gi|61118430|gb|DN559391.1|DN559391
EST:     AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAG                         GTAGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTT
genomic: AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttct ... atgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTT
EST: gi|87152471|gb|DY397260.1|DY397260
EST:     AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAG                         GTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTT
genomic: AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttct ... atgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTT
EST: gi|13126372|gb|BG316942.1|BG316942
EST:     AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAG                         GTGGTAAATAGATATATCGATGAAGGAATTGCAGCAGCTTGTACCTGGTGT
genomic: AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttct ... atgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAG-AGCTTGTACCTGGTGT
EST: gi|93284661|gb|EB676925.1|EB676925
EST:     AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAG                         GTGGTAAATAGATATATCGATGAAGGAATTGC
genomic: AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttct ... atgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGC
EST: gi|61118429|gb|DN559390.1|DN559390
EST:     AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAG                         GTAGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTT
genomic: AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttct ... atgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTT
EST: gi|31612366|gb|CD568988.1|CD568988
EST:     AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAG                         GTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTT
genomic: AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttct ... atgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTT
EST: gi|213174323|gb|FM191608.1|FM191608
EST:     AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAG                         GTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTT
genomic: AACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttct ... atgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTT

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: 246

TCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttct ... atgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

TCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttct ... atgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 116

TCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttct ... atgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 144

TCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttct ... atgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttggataaccatataagaattttcagctggtttttaattttatatgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG
                                 ttttaat  putative branch site (score: 144)
                                tttttaattttatatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttcttctttttgactaccattttttttagtttcttaggcagtatcaaatttggataaccatataagaattttcagctggtttttaattttatatgatgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT