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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcaaggctgtctaaattatgtacctgatttccttatatagttatattcatacttgattcgactgtcccattcatatgagctaactaataattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTACACTGTGACACTATTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTC

Basic information

species Zea mays
transcript GRMZM2G144372_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 6
--tgtcaaggctgtctaaattatgtacctgatttccttatatagttatattca--tacttgattcgactgtcccattcatatgagctaactaataattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTACACTGTGACACTATTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTC
  |||      |  |   | ||  |   |||| |  |||  || |  || |    |  |  ||| || ||     ||| | ||| |||| || | |||  ||||||||| || || |||||||| || ||||| ||||| || |||||||||||||| || ||| | ||||||||||||||||||||||||||||||||||| |
cttgtttttttttccagcactacatgt-tgatgtgatta-gtattcgtaattggttgttatatttgagtgcttttttcct-tgaactaattattgatt-tatagGTACCGAGATCGTCTAAAAAACTTTATGAGGACAATGAGTATGCTCTCTACACGGTAACATTGTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCAC
















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|71428528|gb|DR809578.1|DR809578
EST:     ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
EST: gi|40336015|gb|CK370085.1|CK370085
EST:     ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
EST: gi|67038589|gb|CO464901.1|CO464901
EST:     CTCCCANAAAGACTGGCTGTNCA-GCTATGAGACACTTGATACATTTGTG                         GTACCTAAGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
genomic: CTCCCAAAAAGACTGGCTGT-CAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
EST: gi|89758156|gb|DY687449.1|DY687449
EST:     ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
EST: gi|61117885|gb|DN558846.1|DN558846
EST:     ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
EST: gi|148982506|gb|EE028351.2|EE028351
EST:     ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
EST: gi|61117886|gb|DN558847.1|DN558847
EST:     ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGACTATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
EST: gi|31558493|gb|CD527705.1|CD527705
EST:     ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
EST: gi|61117883|gb|DN558844.1|DN558844
EST:     ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
EST: gi|76012958|gb|DT940128.1|DT940128
EST:     ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
EST: gi|67023340|gb|CO452089.1|CO452089
EST:     ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
EST: gi|32910803|gb|CF015615.1|CF015615
EST:     GACTGGCTGTCAAGCTGTGAGACACTTGATACATTTGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
genomic: GACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
EST: gi|67010828|gb|CO439577.1|CO439577
EST:     ACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
genomic: ACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
EST: gi|31358589|gb|CD442946.1|CD442946
EST:     ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
EST: gi|67022208|gb|CO450957.1|CO450957
EST:     ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
EST: gi|61117882|gb|DN558843.1|DN558843
EST:     ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTG                         GTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC
genomic: ACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTAC

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: 170

TATGATCACCTCGGAACATCTTGTGACACTTCTTGCAATCGTTCCCAAGTACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTACACTGTGACACTATTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 185

TATGATCACCTCGGAACATCTTGTGACACTTCTTGCAATCGTTCCCAAGTACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTACACTGTGACACTATTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

TATGATCACCTCGGAACATCTTGTGACACTTCTTGCAATCGTTCCCAAGTACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTACACTGTGACACTATTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 268

TATGATCACCTCGGAACATCTTGTGACACTTCTTGCAATCGTTCCCAAGTACTCCCAAAAAGACTGGCTGTCAAGCTATGAGACACTTGATACATTTGTGgtaaggttaa ... aattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTACACTGTGACACTATTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcatacttgattcgactgtcccattcatatgagctaactaataattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTACACTGTGACACTATTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTC
                                      aactaat  putative branch site (score: 268)
                                     taactaataattacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcaaggctgtctaaattatgtacctgatttccttatatagttatattcatacttgattcgactgtcccattcatatgagctaactaataattacatagGTACCTAGGTCATCTAAAAAGCTCTATGAAGACAACGAATATGCTCTCTACACTGTGACACTATTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTC

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