Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagcaacttccttctgtagatcagtacttttatagtattaaggacaagcaatatgtatattcacttgaaccattcaaattataagcgttgaagcacgtcaatcatgtgaagatcttaattattgcacggctaatttttggaggcagctgaacctttcactaatgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGATCCGGAGCATGAGGAACGGCTGAAGATGCTGAAGCTTCTTTAGAGAGAAA

Basic information

species Zea mays
transcript GRMZM2G044569_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044569_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g29590.1 (Oryza sativa), 3'ss of exon 6
gcaagcaacttccttctgtagatcagtacttttatagtattaaggacaagcaatatgtatattcacttgaaccattcaaattataagcgttgaagcacgtcaatcatgtgaagatcttaattattgcacggctaatttttggaggcagctgaacctttcactaatgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGATCCGGAGCATGAGGAACGGCTGAAGATGCTGAAGCTTCTTTAGAGAGAAA
                                                            | || ||   |||| |    || |||    |||      || | ||    ||   |||||   ||| |     |   | |      |       | |||| | || |||||||||| |||||||||||||| ||||| |||| ||||||  | |||||||||||||| ||||||||||| |||||||| ||||||||||| || |||      |
------------------------------------------------------gcaagaactccctcagaccagtgctcttctaa----tgacaatgatccagca---aaatgccttaacatttggatattcagaatatctctctaagatgtgcattcattcat-atatgcagGAGTACGTGGTGGAAGATCTTCATGGCAGCTACACGCCACCGAAGCTTGATCCAGAGCATGAGGAGCGGCTGAAAATGCTGAAGCTCCTCTAGCCTCTCA
















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|60400233|gb|DN233040.1|DN233040
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACCCGGTGGAAGACCTTCACGGCAACTCCACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|67014989|gb|CO443738.1|CO443738
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|226431289|gb|GO477625.1|GO477625
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|86466823|gb|DY233193.1|DY233193
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|76913906|gb|DV165315.1|DV165315
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|4776418|gb|AI665421.1|AI665421
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|94474605|gb|EB703563.1|EB703563
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|37621915|gb|CF674968.1|CF674968
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|60352003|gb|DN218976.1|DN218976
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|78025929|gb|DV494316.1|DV494316
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|71764259|gb|DR962196.1|DR962196
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|67013125|gb|CO441874.1|CO441874
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|91877669|gb|EB407626.1|EB407626
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCCCGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|211031776|gb|FL480590.1|FL480590
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|76287271|gb|DV026839.1|DV026839
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|91875639|gb|EB405596.1|EB405596
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|60350312|gb|DN217285.1|DN217285
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|213169179|gb|FM192333.1|FM192333
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|74242906|gb|DT650820.1|DT650820
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|78085524|gb|DV513917.1|DV513917
EST:     GGATTTGGCAGAGGCACTATCACATCCTGCCCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|21395209|gb|BQ539639.1|BQ539639
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
EST: gi|76913907|gb|DV165316.1|DV165316
EST:     GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAG                         GAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT
genomic: GGATTTGGCAGAGGCACTATCACATCCTGACCAAAAGGGAGTTGACAAAGgcaagcaact ... tgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attattgcacggctaatttttggaggcagctgaacctttcactaatgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGATCCGGAGCATGAGGAACGGCTGAAGATGCTGAAGCTTCTTTAGAGAGAAA
                                       cactaat  putative branch site (score: 2)
             taattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagcaacttccttctgtagatcagtacttttatagtattaaggacaagcaatatgtatattcacttgaaccattcaaattataagcgttgaagcacgtcaatcatgtgaagatcttaattattgcacggctaatttttggaggcagctgaacctttcactaatgatatgcagGAATACGTGGTGGAAGACCTTCACGGCAACTACACAGCGCCGAAGCTTGATCCGGAGCATGAGGAACGGCTGAAGATGCTGAAGCTTCTTTAGAGAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC