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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataagttgatctccttttgtattcagagtatagctgataaccatcatgaaaaaatcagcatggtatacaaagatgcgattaactttgctctatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCTGCTTATCCTACACCAAAGTGTGAAAAGAAATGCAAGGAGCAGAACCAAG

Basic information

species Zea mays
transcript GRMZM2G108849_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108849_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g24550.4 (Oryza sativa), 3'ss of exon 8
------------------------------------------ataagttgatc-tccttttgtat-tcagagtatagctgataaccatcatgaaa--aaatcagcatggtatacaaagatgcgattaactttgctctatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCTGCTTATCCTACACCAAAGTGTGAAAAGAAATGCAAGGAGCAGAACCAAG
                                          || |        |  |  | ||| | |   | |   |     |       | |  |  ||||| || |||||  |||        | ||| |  | | |||||||| ||||||||||| || | ||||||||| |||||||| ||||||||||||||||||||||| |||  ||| || ||||||||||||| |||||||||||
gtattgtccattttctacatgctatgacatgaatgtttctgcatgatccagcagtaatcctatatgtgaatatttttttcccggctcctgcaacattagttcagcttgatatactcagaaaatgcacattttccattgttttgcagTGCGATCCATACTTTGATCAGGTCGGTTGTAAGCATCCAGGATGCGAACCTGCTTATCCTACGCCAGTGTGCGAGAAGAAATGCAAGGTGCAGAACCAAG
















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|76282755|gb|DV022323.1|DV022323
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|33104176|gb|CF064136.1|CF064136
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|31354590|gb|CD438947.1|CD438947
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|211491805|gb|FL092420.1|FL092420
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTSRACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|213184041|gb|FM183748.1|FM183748
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|78022002|gb|DV490389.1|DV490389
EST:     GTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: GTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|60357237|gb|DN224210.1|DN224210
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|31355458|gb|CD439815.1|CD439815
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|33100519|gb|CF060479.1|CF060479
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|18963343|gb|BM660382.1|BM660382
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|60353949|gb|DN220922.1|DN220922
EST:     TTGTTC-AAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: TTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|33092955|gb|CF052949.1|CF052949
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|60345830|gb|DN212803.1|DN212803
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|211491801|gb|FL092416.1|FL092416
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|14191380|gb|BG833610.1|BG833610
EST:     CTATAGAGGCATGGCGCTACTTTGGTCAAAATGGTGTTGGTACGGATGAG                         TGTGATCCATACTTCGACC
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACC
EST: gi|14203538|gb|BG837215.1|BG837215
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|60395804|gb|DN228674.1|DN228674
EST:     AATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: AATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|14191381|gb|BG833611.1|BG833611
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|18385054|gb|BM418253.1|BM418253
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAA-GGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGAG-CGGTTGCAAGCATCCTGGATGCGAACC
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCG-GTCGGTTGCAAGCATCCTGGATGCGAACC
EST: gi|33101185|gb|CF061145.1|CF061145
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|211439270|gb|FL284637.1|FL284637
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCTTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|60400644|gb|DN233451.1|DN233451
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|60338736|gb|DN205709.1|DN205709
EST:     TTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: TTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|211042388|gb|FL284655.1|FL284655
EST:     TATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGGATGAG                         TGTGATCCATACTTCGNACCCGGTCGGTTGCAAGCATCCTGGATGCGAAC
genomic: TATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGG-ATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCG-ACCCGGTCGGTTGCAAGCATCCTGGATGCGAAC
EST: gi|14203094|gb|BG836771.1|BG836771
EST:     CTATAGARGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|17970178|gb|BM276943.1|BM276943
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|33093900|gb|CF053894.1|CF053894
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|6012616|gb|AW062053.1|AW062053
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|60350570|gb|DN217543.1|DN217543
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|211488924|gb|FL092409.1|FL092409
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|211486033|gb|FL092385.1|FL092385
EST:     CTAC-TTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|5296139|gb|AI783014.1|AI783014
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCT
EST: gi|18963341|gb|BM660381.1|BM660381
EST:     CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAG                         TGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAAACC
genomic: CTATAGAGGCATGGCGCTACTTTGTTCAAAATGGTGTTGTTACGGATGAGgtataggtct ... tatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAA-CC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaaaaaatcagcatggtatacaaagatgcgattaactttgctctatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCTGCTTATCCTACACCAAAGTGTGAAAAGAAATGCAAGGAGCAGAACCAAG
                               gattaac  putative branch site (score: 2)
                                     ctttgctct  CT-rich tract
                                attaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataagttgatctccttttgtattcagagtatagctgataaccatcatgaaaaaatcagcatggtatacaaagatgcgattaactttgctctatgttgcagTGTGATCCATACTTCGACCCGGTCGGTTGCAAGCATCCTGGATGCGAACCTGCTTATCCTACACCAAAGTGTGAAAAGAAATGCAAGGAGCAGAACCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG