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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattagaatcccaaactgattaatttcttcaatatatctggtttccatacgaaatttaaaaatattgagtgcataaagtagatattttattgttcctgttattttactgaaagtattattaatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG

Basic information

species Zea mays
transcript GRMZM2G035595_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035595_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g16600.1 (Oryza sativa), 3'ss of exon 6
gtattagaatcccaaactgattaatttcttcaatatatctggtttccatacgaaatttaaaaatattgagtgcataaagtagatattttattgttcctgttattttactga--------aagtattattaatct----------tttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG
|||||  ||||||| |    | |  || ||| | | || |   |      || ||  ||||| |  ||||   |||||||| | |  | | | ||  | || |||| || |        || |   ||||  ||          || |||||| ||| |||||||| ||| ||||||||||| |||||||||| ||| ||| || ||| |||||||| ||| |||||||||||||||||||||| ||||
gtattgaaatcccagatctgtgatgtttttctacagatataaatattcatcggaagctaaaatttctgaggcgataaagtaaagaagtcactattgtttttgttttgctaacataatgtaattgacattacactggcaaatgatttcagGGTGTACTAACCTATGGAAAAATTGGTGAATGGAGATTTGACAAGAGAGCATACCAAGACAGGCCACCGCCACGAAATCTTACATTGCCCCCTCCAGGAG

upper sequence: GRMZM2G035595_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G26610.1 (Glycine max), 3'ss of exon 7
gtattagaatcccaaactgattaatttcttcaatatatctggtttccatacgaaatttaaaaatattgagtgcataaagtagatattttattgttcctgttattttactgaaagtattattaatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG
                   | |  || ||| |  | || |  |||   |   | | |  |   |  ||    |||  | |  ||||||     | |  ||| | | |   | ||| ||       | | |||||||| |||| ||||| ||||||||||||||| ||||||||||||| ||    | |    | || ||||||| |||  |  |  ||||||| || || |
-------------------act--ttgctttagcagatatacttttattggaacactgtagcttcctg---tcatctattgtatatttc----tcctagttgtctca---atagtgtttcatgattctcagGGTGAATTGACTTATGGCAAAGTTGGTGAATGGAGATTTGACAAAAGGTCGCATCTACGAGGACCTCCACCAAAAAACTTGCCCCTGCCCCCACCAGGGG

upper sequence: GRMZM2G035595_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv13s0084g00830.t01 (Vitis vinifera), 3'ss of exon 6
gtattagaatcccaaactgattaatttcttcaatatatctggtttccatacgaaatttaaaaatattgagtgcataaagtagatattttattgttcctgttattttactgaaagtattattaatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG
          |    ||||  |  | || ||  ||| | ||| |  |   | || ||       |||  |||      |||    || | | |||        | |  | ||||| || || || ||  ||||||| ||||| ||||| ||| |||| || |||||||||||||| ||||||| || |  | | || || || ||||| ||| | ||||| ||||| || |
----------ctattactggctcttatcatcgttatgtttgggtatc--cctaagttcg----cattttgtg------gtattggttctgtggtta-------tctgttcaaagt-ttcttgatattc-agGGTGAGCTGACATATGGGAAAATTGGAGAGTGGCGATTTGACAAGAGATCATACCTACGTGGACCTCCTCCTAGAAACCTTTCCTTGCCGCCTCCAGGGG

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|86472181|gb|DY238551.1|DY238551
EST:     AGAATACATTTATAATCCACTTCACTTATGGATGTGACTACTCACTAAAG                         GGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCA
genomic: AGAATACATTTATAATCCACTTCACTTATGGATGTGACTACTCACTAAAGgtattagaat ... aatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCA
EST: gi|211246948|gb|FL479530.1|FL479530
EST:     AGAATACATTTATAATCCACTTCACTTATGGATGTGACTACTCACTAAAG                         GGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCA
genomic: AGAATACATTTATAATCCACTTCACTTATGGATGTGACTACTCACTAAAGgtattagaat ... aatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCA
EST: gi|211541587|gb|FL476015.1|FL476015
EST:     AGAATACATTTATAATCCACTTCACTTATGGATGTGACTACTCACTAAAG                         GGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCA
genomic: AGAATACATTTATAATCCACTTCACTTATGGATGTGACTACTCACTAAAGgtattagaat ... aatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCA
EST: gi|211025730|gb|FL435838.1|FL435838
EST:     AGAATACATTTATAATCCACTTCACTTATGGATGTGACTACTCACTAAAG                         GGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCA
genomic: AGAATACATTTATAATCCACTTCACTTATGGATGTGACTACTCACTAAAGgtattagaat ... aatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCA

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: 30 (upstream exon), 47 (downstream exon)
Score: 6

CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTATGGATGTGACTACTCACTAAAGgtattagaat ... aatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 54

CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTATGGATGTGACTACTCACTAAAGgtattagaat ... aatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 37

CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTATGGATGTGACTACTCACTAAAGgtattagaat ... aatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 969

CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTATGGATGTGACTACTCACTAAAGgtattagaat ... aatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtagatattttattgttcctgttattttactgaaagtattattaatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG
                                         tattaat  putative branch site (score: 969)
                                               tctttt  CT-rich tract
                       ttattttactgaaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattagaatcccaaactgattaatttcttcaatatatctggtttccatacgaaatttaaaaatattgagtgcataaagtagatattttattgttcctgttattttactgaaagtattattaatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA