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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatgtatatatatgatatagtcgagctgtgaaatgtacgtatgcattgcattgcattgcatgcatggtgatagagatagatccagtctctcttgctggctggttttaatttgctaacgtacgtacactgacgacgacgacgaccacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATGGGCCTGTTCGAGAAGCGGCGCGCCCGGAAGTTCTTCATATACGTGCAGG

Basic information

species Zea mays
transcript GRMZM2G084440_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G084440_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g16900.1 (Oryza sativa), 3'ss of exon 4
gtatatatgtatatatatgatatagtcgagctgtgaaatgtacgtatgcattgcattgcattgcatgcatggtgatagagatagatccagtctctc--ttgctggctggttttaatttgctaacgtacgtacactgacgacgacgacgaccacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATGGGCCTGTTCGAGAAGCGGCGCGCCCGGAAGTTCTTCATATACGTGCAGG
                                       ||  | ||    |   |   ||   |||||   ||  | | || | | || | |||   || |||  |    || ||||| |                       | |||   ||||||||||||||||| || ||||| || || |||||| | || || || || |||||||| || || ||||| || ||  |||| |||||||||||||||||||
---------------------------------------gtgtggatctgatat-tcatatgttatgca-actgtcaaacattggtgcattttctgaattactgagtcacctttatttgtt----------------------tggcgataccgacagATCCACAAAGTTCCTGCAACTGATGTCGAGGCCTTGAAATCTAATCTAATGGGCCTTTTTGAAAAGCGCCGTGCTAGGAAATTCTTCATATACGTGCAGG

upper sequence: GRMZM2G084440_T01 (Zea mays), 3'ss of exon 4
lower sequence: EDP02072 (Chlamydomonas reinhardtii), 3'ss of exon 6
gtatatatgtatatatatgatatagtcgagctgtgaaatgtacgtatgcattgcattgcattgcatgcatggtgatagagatagatccagtctctcttgctggctggttttaatttgctaacgtacgtacactgacgacgacgacgaccacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATGGGCCTGTTCGAGAAGCGGCGCGCCCGGAAGTTCTTCATATACGTGCAGG
                                                |||  ||   |    ||||| || ||||   |           | ||  |||||   ||||     |  | |   |||  |||||  | ||   | | |||||       |||||  || ||||| | ||||  |||||| ||    |||   ||||||||||||||||||||||| ||||| || || |||||| |           
-----------------------------------------------ccatgccaaaccggcacatgcctgctgatgccg-----------cgctgctgctg--cggttggtgctgcccatactacccacactacccacactgcccaccact----ggccacag-
















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|211419516|gb|FL330470.1|FL330470
EST:     ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAG                         ATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
genomic: ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAGgtatatatgt ... accacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
EST: gi|78119657|gb|DV538041.1|DV538041
EST:     ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAG                         ATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
genomic: ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAGgtatatatgt ... accacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
EST: gi|78108949|gb|DV527366.1|DV527366
EST:     ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAG                         ATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
genomic: ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAGgtatatatgt ... accacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
EST: gi|211267087|gb|FL311760.1|FL311760
EST:     ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAG                         ATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
genomic: ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAGgtatatatgt ... accacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
EST: gi|6827020|gb|AW330663.1|AW330663
EST:     ACCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAG                         ATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
genomic: ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAGgtatatatgt ... accacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
EST: gi|50324747|gb|CO519873.1|CO519873
EST:     ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAG                         ATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
genomic: ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAGgtatatatgt ... accacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
EST: gi|211349904|gb|FL349175.1|FL349175
EST:     ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAG                         ATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
genomic: ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAGgtatatatgt ... accacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
EST: gi|78179007|gb|DV549380.1|DV549380
EST:     ACCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAG                         ATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
genomic: ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAGgtatatatgt ... accacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
EST: gi|12045994|gb|BF728029.1|BF728029
EST:     ACCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAG                         ATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
genomic: ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAGgtatatatgt ... accacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
EST: gi|211226808|gb|FL338396.1|FL338396
EST:     ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAG                         ATCCACAAAGTCCCGGCAACCGACGTGGGAGGCCCTCAAAGTCGAACCTGA
genomic: ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAGgtatatatgt ... accacgacagATCCACAAAGTCCCGGCAACCGACGTGG-AGGCCCTCAA-GTCGAACCTGA
EST: gi|211447007|gb|FL349613.1|FL349613
EST:     ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAG                         ATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
genomic: ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAGgtatatatgt ... accacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
EST: gi|211436016|gb|FL361907.1|FL361907
EST:     ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAG                         ATCCACAAAGTCCCGGCAACCGACGTGGAGGCC-TCAAGTCGAACCTGATG
genomic: ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAGgtatatatgt ... accacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
EST: gi|78093304|gb|DV521678.1|DV521678
EST:     ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAG                         ATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG
genomic: ATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAGgtatatatgt ... accacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATG

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 2 RNA-Seq libraries.


Block sizes: 27 (upstream exon), 23 (downstream exon)
Score: 1

GGCAAACGGCGCGCTGGTCCGCGTCCTGATCCGCACCAGCGTGACCAAGTATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAGgtatatatgt ... accacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATGGGCCTGTTCGAGAAGCGGCGCGCCCGGAAGTTCTTCATATACGTGCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 339

GGCAAACGGCGCGCTGGTCCGCGTCCTGATCCGCACCAGCGTGACCAAGTATCTCAACTTCAAGGCTGTTGACGGGAGCTTTGTGTACAACAATGGCAAGgtatatatgt ... accacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATGGGCCTGTTCGAGAAGCGGCGCGCCCGGAAGTTCTTCATATACGTGCAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctggttttaatttgctaacgtacgtacactgacgacgacgacgaccacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATGGGCCTGTTCGAGAAGCGGCGCGCCCGGAAGTTCTTCATATACGTGCAGG
      ttttaatttgctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatatgtatatatatgatatagtcgagctgtgaaatgtacgtatgcattgcattgcattgcatgcatggtgatagagatagatccagtctctcttgctggctggttttaatttgctaacgtacgtacactgacgacgacgacgaccacgacagATCCACAAAGTCCCGGCAACCGACGTGGAGGCCCTCAAGTCGAACCTGATGGGCCTGTTCGAGAAGCGGCGCGCCCGGAAGTTCTTCATATACGTGCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC