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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtttggtatccaccacataaattaatgctcaattattgtttagtcacttaacagactatactgaatataggcctgaaagaggaatcactaagagcatcacgtacatgaatacagcaatggagtattattactaaagttctattatatatgagaacacacctgactaaatgtgcttatttattcttggcaccagGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGGAAATTTTGGGGAGACAGCAATCTAAAGAGCAAATTCTGGGGACAATCCA

Basic information

species Zea mays
transcript GRMZM2G409265_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G409265_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g40590.1 (Oryza sativa), 3'ss of exon 5
gtcagtttggtatccaccacataaattaatgctcaattattgtttagtcacttaacagactatactgaatataggcctgaaagaggaatcactaagagcatcacgtacatgaatacagcaatggagtattattactaaagttctattatatatgagaacacacctgactaaatgtgcttatttattcttggcaccagGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGGAAATTTTGGGGAGACAGCAATCTAAAGAGCAAATTCTGGGGACAATCCA
                                                                                            ||| ||   ||   ||     |   || | ||   |||| || |     |    || || | | |  |||  ||| | ||| || |  |||||||||| |||||||| ||||||||||| |||||||||||||| || ||||| ||||||||||||||||||||||| ||||||||||||||||||||||| ||||| || ||||
--------------------------------------------------------------------------------------------taaaagtggcagacactgttctgatgcca-ggcacattaatatt----cttctctacatttcacacaacatatgagttaatttgttagtttattcttgtcaccagGTTAGTCATCATCCGATGGTCATGGCATGCCATTGTGAAGGGAAAGGTTGGAAATTTTGGGGTGACAGCAATCTAAAGAGCAAATTTTGGGGGCAGTCCA

upper sequence: GRMZM2G409265_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
gtcagtttggtatccaccacataaattaatgctcaattattgtttagtcacttaacagactatactgaatataggcctgaaagaggaatcactaagagcatcacgtacatgaatacagcaatggagtat-tattactaaagttctattatatatgagaacacacctga-ctaaatgtgcttatttattcttggcacc----agGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGGAAATTTTGGGGAGACAGCAATCTAAAGAGCAAATTCTGGGGACAATCCA
    || || |||        |     | ||    ||  || ||| ||  ||||     || |      |||  ||||   ||  ||||   | | | |   |  |    | ||       | |  | | | ||| || |  | |    |      ||||  |  ||| || ||  |  || ||| |  ||  || |    |||| || |||||||| ||| |  ||||||||||||| ||||| | ||| |||||||||||||| ||||||||  | || ||||| || ||||| |  || |
----gtgtgatatggtttttgttttcaattgtatgatgctt-ttttgtgtcttatggacctgtcgcatctattagccttgtagctgaatt-ttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA

upper sequence: GRMZM2G409265_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 3'ss of exon 5
gtcagtttggtatccaccacataaattaatgctcaattattgtttagtcacttaacagactatactgaatataggcctgaaagaggaatcactaagagcatcacgtacatgaatacagcaatggagtattattactaaagttctattatatatgagaacacacctgactaaatgtgct-tatttattcttggcac--cagGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGGAAATTTTGGGGAGACAGCAATCTAAAGAGCAAATTCTGGGGACAATCCA
                                                                                                      |  ||      | || |      ||  |||   |  || | ||   ||  | | |    | |    |  || | || | |   | | | ||    ||||| ||||||||||| ||| |  |||||||||| || ||||| | ||| |||||||| ||||| ||||||||| | || ||||| || ||||| |  || |
----------------------------------------------------------------------------------------------------ggagatattaatttgcaacctctttgtcatatctttcgagctttagattaagtaaaagttaatcatcttgcatcttctatctccctacgttgctttgcagGTGAGTCATCATCCAATGATTGTGGCATGTCATTGCGAGGGCAGAGGCTGGAAATTCTGGGGTGACAGCAATTTGAAAAGCAAGTTTTGGGGTCGTTCAA

upper sequence: GRMZM2G409265_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S427_40V6.1 (Physcomitrella patens), 3'ss of exon 5
gtcagtttggtatccaccacataaattaatgctcaattattgtttagtcacttaacagactatactgaatataggcctgaaagaggaatcactaagagcatcacgtacatgaatacagcaatggagtattattactaaagttctattatatatgagaacacacc-tgactaaatgtgcttatttattcttggcaccagGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGGAAATTTTGGGGAGACAGCAATCTAAAGAGCAAATTCTGGGGACAATCCA
                         || | ||   ||| |  |||  ||  ||    ||| ||      ||   | ||||  ||     |||         | |  | |||  |   | | | | |  | ||  |||| |    ||| ||  |  ||    ||  | | ||  ||   |  | | || |  |   ||||| || ||||| || ||| || ||||||||||||| |||||   ||| |||||||| ||||||||||||||  | || ||||| || ||||| |  || |
-----------------------gtttgacgc--gattgtcattt--tctattgtttgacaatctct--taggagtctgatggaattgccacatttgttcgcgccgagatgtttctggtacttgtgcttcatctctaagg---aattgtaggttggactgaactataattatctgaaatcctctgttttgcggcgcagGTGAGCCATCACCCAATGATCGTGGCATGTCACTGCGAGGGTCGAGGATGGAAATTCTGGGGAGACAGCAACTTGAAAAGCAAGTTTTGGGGTCGTTCTA

upper sequence: GRMZM2G409265_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ15167 (Selaginella moellendorffii), 3'ss of exon 5
gtcagtttggtatccaccacataaattaatgctcaattattgtttagtcacttaacagactatactgaatataggcctgaaagaggaatcactaagagcatcacgtacatgaatacagcaatggagtattattactaaagttctattatatatgagaacacacctgactaaatgtgcttatttattcttggcaccagGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGGAAATTTTGGGGAGACAGCAATCTAAAGAGCAAATTCTGGGGACAATCCA
                                                                                                                                |||       |||| | || | | ||            |||  |||    | ||  |  |  | || |||||||||| ||||| |||||  | || ||||||||||||||    || |||||| | ||||| ||||||||||||||||| ||||| ||||| |  || |
-------------------------------------------------------------------------------------------------------------------------------gttagccagtcagtttttttttctctg----------ctacttgatgctgattttcttcgtctgtac-agGTCAGTCACCATCCCATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA

upper sequence: GRMZM2G409265_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 6
gtcagtttggtatccaccacataaattaatgctcaattattgtttagtcacttaacagactatactgaatataggcctgaaagaggaatcactaagagcatcacgtacatgaatacagcaatggagtattattactaaagttctattatatatgagaacacacctgactaaatgtgcttatttattcttggcaccagGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGGAAATTTTGGGGAGACAGCAATCTAAAGAGCAAATTCTGGGGACAATCCA
                                                                                                                                |||       || | | || | |          || |||   | ||   || ||  |   |     ||||||||||| ||||| |||||  | || ||||||||||||||    || |||||| | ||||| ||||||||||||||||| ||||| ||||| |  || |
-------------------------------------------------------------------------------------------------------------------------------gttagctagtcagcttttttctctgc-------tacttgat--actgattttcttcgtctgta----cagGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA

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|211525268|gb|FL432923.1|FL432923
EST:     CCTATGAAGCTGATTACCCTGAAAAGGGGATCCGTTTCTTCTCTGAGAAG                         GTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGG
genomic: CCTATGAAGCTGATTACCCTGAAAAGGGGATCCGTTTCTTCTCTGAGAAGgtcagtttgg ... ttggcaccagGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGG
EST: gi|60346794|gb|DN213767.1|DN213767
EST:     TTCTTTGAGAAG                         TTCAGTCATCATCCTATTGTCATTGGCATGTCACTGTGAGGGGAAAGGTTG
genomic: TTCTCTGAGAAGgtcagtttgg ... ttggcaccagGTCAGTCATCATCCTATGGTCA-TGGCATGTCACTGTGAGGGGAAAGGTTG
EST: gi|60344714|gb|DN211687.1|DN211687
EST:     CNTATGAAGCTGATTACCCTGAAAAGGGGATCCGTTTCTTCTCTGAGAAG                         GTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGG
genomic: CCTATGAAGCTGATTACCCTGAAAAGGGGATCCGTTTCTTCTCTGAGAAGgtcagtttgg ... ttggcaccagGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGG
EST: gi|60344453|gb|DN211426.1|DN211426
EST:     CCTATGAAGCTGATTACCCTGAAAAGGGGATCCGTTTCTTCTCTGAGAAG                         GTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGG
genomic: CCTATGAAGCTGATTACCCTGAAAAGGGGATCCGTTTCTTCTCTGAGAAGgtcagtttgg ... ttggcaccagGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattatatatgagaacacacctgactaaatgtgcttatttattcttggcaccagGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGGAAATTTTGGGGAGACAGCAATCTAAAGAGCAAATTCTGGGGACAATCCA
                       gactaaa  putative branch site (score: 2)
                                      tttattctt  putative PPT
                                   ttatttattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtttggtatccaccacataaattaatgctcaattattgtttagtcacttaacagactatactgaatataggcctgaaagaggaatcactaagagcatcacgtacatgaatacagcaatggagtattattactaaagttctattatatatgagaacacacctgactaaatgtgcttatttattcttggcaccagGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGGAAATTTTGGGGAGACAGCAATCTAAAGAGCAAATTCTGGGGACAATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA