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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattggctggattcttcttttaactatttcttttgccataattaacctcctaaaacttcattctactattattttggcacaaaacacacatacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCGAAGGATGAGGATGACAGCGGAGGCGAGGAAGAGGAGGAAGAGGAAGATC

Basic information

species Zea mays
transcript GRMZM2G008259_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008259_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g14010.1 (Oryza sativa), 3'ss of exon 4
gtatgattggctggattcttcttttaacta--tttcttttgccataattaacctcctaaaacttcattctactattattttggcacaaaacacacatacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCGAAGGATGAGGATGACAGCGGAGGCGAGGAAGAGGAGGAAGAGGAAGATC
   | || |  || || ||| |  | |||   || |||||| ||| |  |    |  | ||| | ||           |||||||| |||||  |       |||||  | |||||||| ||||||||||| |||||| | ||||||||||||||||||||||||||||| |||||||| ||||||||||||||||| |||||||
--gtaat-gaatgaatccttttaattactgtgttccttttggcatgaaaatgagctcataacatgatgtc-------ctttggcaccaaacattccc-----cagCCATCGCGCCAGCCGGAACCCAACTCTAGGGGTCCAAAGATGCCACCTCCGAAGGATGAGGATGATAGCGGAGGTGAGGAAGAGGAGGAAGAAGAAGATC
















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|78544063|gb|DV621561.1|DV621561
EST:     AGGAGAAAACTCCCAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|60394906|gb|DN227775.1|DN227775
EST:     AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|5069903|gb|AI737868.1|AI737868
EST:     GCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: GCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|71766892|gb|DR964829.1|DR964829
EST:     AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|60350037|gb|DN217010.1|DN217010
EST:     AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|31664355|gb|CD573080.1|CD573080
EST:     GGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCNCCTCCG
genomic: GGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|60341456|gb|DN208429.1|DN208429
EST:     AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         A
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacag-
EST: gi|60341456|gb|DN208429.1|DN208429
EST:     AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         A
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacag-
EST: gi|17932344|gb|BM269304.1|BM269304
EST:     AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|78544023|gb|DV621521.1|DV621521
EST:     AGGAGAAAACTCCCAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|26455859|gb|CA827442.1|CA827442
EST:     AGGAGAAAACTCCCAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|60397347|gb|DN230163.1|DN230163
EST:     AAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: AAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|149070147|gb|EE158548.2|EE158548
EST:     AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTGGAAGATGCCACCTCCG
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|19822278|gb|BQ048302.1|BQ048302
EST:     AGGAGAAAACTCCCAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|4804186|gb|AI666052.1|AI666052
EST:     AAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAN                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: AAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|60401383|gb|DN234190.1|DN234190
EST:     CGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: CGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|50337531|gb|CO532657.1|CO532657
EST:     AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|149106606|gb|EE188499.2|EE188499
EST:     AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTGGAAGATGCCACCTCCG
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|71775176|gb|DR973054.1|DR973054
EST:     AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|211244489|gb|FL128350.1|FL128350
EST:     AGGAGAAAACTCCCAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|166556874|gb|EG264754.1|EG264754
EST:     AGGAGAAAACTCCCAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGA
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGA
EST: gi|149113200|gb|EE182185.2|EE182185
EST:     AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTTGAAGATGCCACCTCCG
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|74236626|gb|DT644540.1|DT644540
EST:     GCAAGAGCAATAAAGGTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCGG
genomic: GCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|22546373|gb|BU098684.1|BU098684
EST:     AGGAGAAAACTCCCAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
genomic: AGGAGAAAACTCCGAAAAGCAGCAGCAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG
EST: gi|89247144|gb|DY618930.1|DY618930
EST:     CAAGAGCAATAAAGCTGGCCCAAAA                         CCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTGGAAGATGCCACCTCCG
genomic: CAAGAGCAATAAAGCTGGCCCAAAAgtatgattgg ... atacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctcctaaaacttcattctactattattttggcacaaaacacacatacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCGAAGGATGAGGATGACAGCGGAGGCGAGGAAGAGGAGGAAGAGGAAGATC
   tcctaaa  putative branch site (score: 2)
               attctactattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgattggctggattcttcttttaactatttcttttgccataattaacctcctaaaacttcattctactattattttggcacaaaacacacatacatacagCCGCCACGCCAGCCAGAACCCAACTCAAGGGGTTCGAAGATGCCACCTCCGAAGGATGAGGATGACAGCGGAGGCGAGGAAGAGGAGGAAGAGGAAGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA