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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagattccactgcctcccacctcctattgtgtttttgcttcaagccttcacttatttccttttctctgttctatgtaatcttattggtttggttaatgccatggtatttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG

Basic information

species Zea mays
transcript GRMZM2G008623_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008623_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g59600.1 (Oryza sativa), 3'ss of exon 2
gttagattccactgcctcccacctcctattgtgtttttgcttcaagccttcacttatttccttttctctgttctatgtaatcttattggtttggttaatgccatggtatttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
||| | ||  |||||  |||           | | ||| ||||    |||    ||   | | |||  |  | | || |||  | |         | | |   |  ||||||| ||||||||||||||||| ||||| ||||||||||| || ||||||
gttcggtttaactgctcccc-----------tttctttccttc----cttttgctaccgcttcttcctttctgtgtgcaattatgtaa-------tgacgttctaatatttgttaacagGACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG

upper sequence: GRMZM2G008623_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G14330.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------gttagattccactgcctcccacctcctattgtgtttttgcttcaagccttcacttat-ttccttttctctgttctatgtaatcttattggtttggttaatgccatggtatttgtga-------acagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
                                                ||  | | |   |  |   |  |   |    |  |||  || |    |     ||| ||  |||| | |     || |  |  | || || | | || ||   |   |||||  |        |||||||||| ||||||||||||||||||||||  ||||  ||
gttggtacttatcattattattattattattattattattattatacttttaaattcgtggttttaaaattgaaaaaaagagtttatttaataattatgagtatgttttttttttttaaatgattttgtaatttttgtattggtagtgatcttagatttgaaactttgttgcagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG

upper sequence: GRMZM2G008623_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G17920.1 (Glycine max), 3'ss of exon 1
------------------gttagattccactgcctcccacctcctattgtgtttttgcttcaagccttcacttatttccttttctctgttctatgtaatcttattggtttggt--taatgcca----tggtatttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
                   ||  | | |   |  |   |  |   |  |   |  |   |  |    | |  |  ||  ||||     || | | |  | || |   ||||||  | || | |    ||  | ||      ||||||||| ||||||||||||||||||||||  ||||  ||
gttggtactttttttttttttttaattcgtggttttgaaattgaaacggaaatagtttattgaataatta--tgatttttttttgtgattttgtatttttttttgtatttggtagtgatcctagatttgaaactttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG

upper sequence: GRMZM2G008623_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G27020.1 (Arabidopsis thaliana), 3'ss of exon 1
----gttagattccactgcctc---ccacctcctattgtgtttttgcttcaagccttcacttatttccttttctctgttctatgtaatcttattggtttggttaatg------ccatggtatttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
    ||| | ||   || | ||   |  |  ||| | ||   |  | || | || |      | ||     | |  ||| |    |    |   |||||| | || |      || |  | ||| |   ||||||||||||||| ||||||||||||||||| |||||  ||
gttagttggctttatcttcttcgatcttcgccctttagtagatcggattta-gcttctgaaaactttgagattttggttatcgacacgaattagggtttgttaaaagtctttccctttttttttcttcgcagGACTGTTGTTGGAATCAAGTGCAAAGATGGGATTGTTATG

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|22819364|gb|BU499454.1|BU499454
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|91049728|gb|EB160146.1|EB160146
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|211461819|gb|FL074147.1|FL074147
EST:     GGTCGCGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|211461826|gb|FL074154.1|FL074154
EST:     GGTCGCGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAATGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAA-GTGCAAAGATGGCATTGTCCTG
EST: gi|22819427|gb|BU499517.1|BU499517
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGAT
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGAT
EST: gi|93284362|gb|EB676626.1|EB676626
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|22819362|gb|BU499452.1|BU499452
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|211064278|gb|FK983495.1|FK983495
EST:     GGTCGCGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|211461823|gb|FL074151.1|FL074151
EST:     GGTCGCGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|211064280|gb|FK983497.1|FK983497
EST:     GGTCGCGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|78106193|gb|DV524611.1|DV524611
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|22819430|gb|BU499520.1|BU499520
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|71431491|gb|DR812541.1|DR812541
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|21843523|gb|BQ704104.1|BQ704104
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|148931430|gb|EC874390.2|EC874390
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|211064283|gb|FK983500.1|FK983500
EST:     GGTCGCGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|50333782|gb|CO528908.1|CO528908
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|211064277|gb|FK983494.1|FK983494
EST:     GGTCGCGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|26456267|gb|CA827850.1|CA827850
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|148981882|gb|EE027956.2|EE027956
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|211464348|gb|FL074165.1|FL074165
EST:     GGTCGCGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|5566922|gb|AI881833.1|AI881833
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|19770380|gb|BQ035101.1|BQ035101
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|149084419|gb|EE173874.2|EE173874
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
EST: gi|148949932|gb|EC895439.2|EC895439
EST:     GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGG                         GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
genomic: GGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattcc ... ttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctgttctatgtaatcttattggtttggttaatgccatggtatttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG
                            ggttaat  putative branch site (score: 4)
         tatgtaatcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagattccactgcctcccacctcctattgtgtttttgcttcaagccttcacttatttccttttctctgttctatgtaatcttattggtttggttaatgccatggtatttgtgaacagGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG