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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttacttttctgacaacgttgcatgttacaacacaaataagttttctgcgaccccagaaggtatattcagctctgaacagctttgcctgtaattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTAGTGCTTGGCTACTTGAACAATCTTGTGATCGAAATGGCCTTCTTGGTAC

Basic information

species Zea mays
transcript GRMZM2G069976_T01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069976_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os10g33930.1 (Oryza sativa), 3'ss of exon 8
-cttacttttctgacaacgttgcatgttacaacacaaataagttttctgcgaccccagaaggtatattcagctctgaacagctttgcctgtaattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTAGTGCTTGGCTACTTGAACAATCTTGTGATCGAAATGGCCTTCTTGGTAC
 ||  | || |  | |  ||   |  | |         |||    ||||| |  |     |||| || |||||||||||| |||| | || | |||| ||||||||||||||||| || || ||||| || ||||| |||||||||||||| |||||||||||||||||||| || ||||| |||||||||||| ||||||
actagcgttacaaagattgtctgaaataaatcgtggcgtaatgaatctgccattctgtttggtacatccagctctgaacatctttacatgca-tttttcagCTTGGAGTTGATATAGGCTCGTCAACAGTTGCACGGGGTGTGGTGAGCCTTGTGCTTGGCTACTTGAACAACCTGGTGATTGAAATGGCCTTCCTGGTAC

upper sequence: GRMZM2G069976_T01 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA13G40010.1 (Glycine max), 3'ss of exon 19
----cttacttttctgacaacgttgcatgttacaacacaaataagttttctgcgaccccagaaggtatattcagctctgaacagctttgcctgtaattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTAGTGCTTGGCTACTTGAACAATCTTGTGATCGAAATGGCCTTCTTGGTAC
    ||    ||  |   |    |||||| | || || | ||     | |  | | |    | |  ||  | |  |||| | | | | || |  |||||  |||||||||||||||||||| |||||||| || ||| ||||||| ||||| || || ||||| ||| | ||| |||| || || || ||||| || ||  |||
agaactgggcttaatagtagatatgcatgatgcatcaaacatttagctgcaactatctttcatgtgattctta--tctggaaatcgtggcattcaattt--cagCTTGGAGTTGATATTGGATCATCAACTGTCGCAAGAGGTGTTGTGAGTCTTGTCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATAC

upper sequence: GRMZM2G069976_T01 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA12G29750.1 (Glycine max), 3'ss of exon 19
cttactttt----ctgacaacgttgcatgttacaacacaaataagttttctgcgaccccagaaggtatattcagctctgaacagctttgcctgtaattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTAGTGCTTGGCTACTTGAACAATCTTGTGATCGAAATGGCCTTCTTGGTAC
 | |   ||     | | |    |||||| | || || | ||     | |    | |    | |  ||  | |  |||| | |   | || |  |||||  |||||||||||||||||||| |||||||| || ||| ||||||| ||||| || || ||||| ||| | ||| |||| || || || ||||| || ||  |||
ttaagaattgggcttaatagatatgcatgatgcatcaaacatttagctgcaatcatctttcatgtgattctta--tctggaaattgtggcattcaattt--cagCTTGGAGTTGATATTGGATCATCAACTGTTGCAAGAGGTGTTGTGAGTCTTGTCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATAC

upper sequence: GRMZM2G069976_T01 (Zea mays), 3'ss of exon 20
lower sequence: AT2G28320.1 (Arabidopsis thaliana), 3'ss of exon 19
---------------------cttacttttctgacaacgttgcatgt---tacaacacaaataag-ttttctgcgaccccagaaggtatattcagc---tctgaacagctt---tgcctgtaattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTAGTGCTTGGCTACTTGAACAATCTTGTGATCGAAATGGCCTTCTTGGTAC
                     ||   |  |   |  |  | | || |   ||| |||  | |  |  |||   ||        | | ||  | ||    ||| |     ||     ||||| |||||| |||| || ||||||||||| |||||||| || ||| |||| || ||||| || || ||||| ||| | ||||| || ||||| ||||||||||||||  |||
gtaacacagtaaggattgatgctagatcctaacaggaattagtatctatctaccacaacagtgtgacttttcacgtttgagccacgcattgttagaaaatcttatttttttgtacacctgttattttc-agCTGGGCGTTGATATTGGGTCATCAACTGTTGCAAGAGGAGTTGTGAGTCTTGTTCTTGGTTACCTCAACAAACTCGTGATTGAAATGGCCTTCTTAATAC

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|32838340|gb|CD978018.1|CD978018
EST:     TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAG                         CTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
genomic: TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAGgtaagctata ... aattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
EST: gi|37379498|gb|CF626493.1|CF626493
EST:     TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAG                         CTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
genomic: TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAGgtaagctata ... aattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
EST: gi|71298058|gb|DR785006.1|DR785006
EST:     TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAG                         CTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
genomic: TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAGgtaagctata ... aattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
EST: gi|211124229|gb|FL321156.1|FL321156
EST:     TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAG                         CTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
genomic: TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAGgtaagctata ... aattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
EST: gi|32836585|gb|CD976263.1|CD976263
EST:     TTGGACAAGCATTAGAAATCAATTATTTTCGGGGAAGAAACTATTTGGAG                         CTTGGAGTTGATAT
genomic: TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAGgtaagctata ... aattttccagCTTGGAGTTGATAT
EST: gi|71298057|gb|DR785005.1|DR785005
EST:     TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAG                         CTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
genomic: TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAGgtaagctata ... aattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
EST: gi|211429970|gb|FL331477.1|FL331477
EST:     TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAG                         CTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
genomic: TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAGgtaagctata ... aattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
EST: gi|211520390|gb|FL360200.1|FL360200
EST:     TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAG                         CTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
genomic: TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAGgtaagctata ... aattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
EST: gi|211318393|gb|FL341250.1|FL341250
EST:     TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAG                         CTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
genomic: TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAGgtaagctata ... aattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
EST: gi|211186353|gb|FL348559.1|FL348559
EST:     TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAG                         CTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA
genomic: TTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAGgtaagctata ... aattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTA

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), 43 (downstream exon)
Score: 35

GGATCTTGGATTGTTAAACAGAGTGTGGGCAAGAAAGCTTGCTTGGTTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAGgtaagctata ... aattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTAGTGCTTGGCTACTTGAACAATCTTGTGATCGAAATGGCCTTCTTGGTAC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 30

GGATCTTGGATTGTTAAACAGAGTGTGGGCAAGAAAGCTTGCTTGGTTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAGgtaagctata ... aattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTAGTGCTTGGCTACTTGAACAATCTTGTGATCGAAATGGCCTTCTTGGTAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 35

GGATCTTGGATTGTTAAACAGAGTGTGGGCAAGAAAGCTTGCTTGGTTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAGgtaagctata ... aattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTAGTGCTTGGCTACTTGAACAATCTTGTGATCGAAATGGCCTTCTTGGTAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 22

GGATCTTGGATTGTTAAACAGAGTGTGGGCAAGAAAGCTTGCTTGGTTGGACAAGCATTAGAAATCAATTATTTTCGTGGAAGAAACTATTTGGAGgtaagctata ... aattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTAGTGCTTGGCTACTTGAACAATCTTGTGATCGAAATGGCCTTCTTGGTAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcgaccccagaaggtatattcagctctgaacagctttgcctgtaattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTAGTGCTTGGCTACTTGAACAATCTTGTGATCGAAATGGCCTTCTTGGTAC
                                               ttttcc  CT-rich tract
                                          tgtaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttacttttctgacaacgttgcatgttacaacacaaataagttttctgcgaccccagaaggtatattcagctctgaacagctttgcctgtaattttccagCTTGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTAGTGCTTGGCTACTTGAACAATCTTGTGATCGAAATGGCCTTCTTGGTAC

- - -ttttctg
- - - - - - - - - -tgcatgt
- - - - - - - - - - - - - - caacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctgt