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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAATCTTCTCAAGGGAATACCATTCCTGAAGCCATTTCCCAGTCATTCTAACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgttttatttattgctgcatgtttgcatttccatcttattcctttgaggtatcagtcacttttattgtgatttaaggtcagaaaatattagtgcttgtttttatgcaggaatgtttggaagagtatgcaatttgcagcattactcacatgttttattgacaaaaatttcag

Basic information

species Zea mays
transcript GRMZM2G170595_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170595_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g47940.1 (Oryza sativa), 5'ss of exon 8
TAATCTTCTCAAGGGAATACCATTCCTGAAGCCATTTCCCAGTCATTCTAACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgttttatttattgctgcatgtttgcatttccatcttattcctttgaggtatcagtcacttttattgtgatttaaggtcagaaaatattagtgcttgtttttatgcaggaatgtttggaagagtatgcaatttgcagcattactcacatgttttattgacaaaaatttcag
  |||||||||| | |||||||||||| |||||||||||||| || |||||||| ||||||||||||||||| ||||| || |||||||||||||||||||||||   |  || ||  | | |   | ||||||     | ||  ||||| ||    || | ||| |   |||  |||        || || |     |   ||||   ||| | || |                                                       
CGATCTTCTCAAAGAAATACCATTCCTAAAGCCATTTCCCAGCCACTCTAACTTTATTCTCTGCGAGGTCACATCAGGCAAAGATGCAAAGAAAATAAAGgtttgcactgcttgttagtac-tccctccatttc-----tttttgtttgaagt--tggttagtttgaaattgaactaacc------aacatca-----tacgtttacagaggta-gtata------------------------------------------------------

upper sequence: GRMZM2G170595_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA16G27220.1 (Glycine max), 5'ss of exon 9
TAATCTTCTCAAGGGAATACCATTCCTGAAGCCATTTCCCAGTCATTCTAACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgttttattt-attgctgcatgtttgc-atttccatcttattcctttgaggtatcagtcacttttattgtgatttaaggtcagaaaatattagtgcttgtttttatgcaggaatgtttggaagagtatgcaatttgcagcattactcacatgttttattgacaaaaatttcag
| | ||| | || | | | ||||||||   ||||||||| || ||||||||||||||||| || ||||| || ||||||||||||||||||||  |||||||   ||   ||  ||  || |||   |   | ||     ||||| ||||    | | |   |  |||    |||||   | |  |  |  | |    |                                                                             
TGACCTTTTGAAAGAAGTTCCATTCCTCCGGCCATTTCCAAGCCATTCTAACTTCATTCTTTGTGAGGTTACATCAGGAAAGGATGCAAAGAAGCTAAAGgtaccttcctttccatatcttcatacatattagtttttctttatttctttattttcttataaatatttgggatgattattgtttggtgagcaatttgaca----------------------------------------------------------------------------
















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|71332193|gb|DR803017.1|DR803017
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|26457570|gb|CA829153.1|CA829153
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|21987125|gb|BQ778653.1|BQ778653
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|22543121|gb|BU093559.1|BU093559
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|22472840|gb|BU037320.1|BU037320
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|211376337|gb|FL031210.1|FL031210
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|22542705|gb|BU093143.1|BU093143
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|148929910|gb|EE285675.2|EE285675
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCCCTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|21760175|gb|BQ635716.1|BQ635716
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGG
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGG
EST: gi|89251650|gb|DY623436.1|DY623436
EST:     ACTTCATTTTTTGGGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCCCTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|22473177|gb|BU037657.1|BU037657
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|21759967|gb|BQ635508.1|BQ635508
EST:     ACTTCATTCTCTGCGAGGTCCCGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCCCTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|148974571|gb|EE025360.2|EE025360
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|211376338|gb|FL031211.1|FL031211
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|5847509|gb|AW000588.1|AW000588
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|71328632|gb|DR800986.1|DR800986
EST:     ACTTCATTCTTTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|22542058|gb|BU092496.1|BU092496
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|89246826|gb|DY618613.1|DY618613
EST:     ACCTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|71758874|gb|DR956811.1|DR956811
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|78021500|gb|DV489887.1|DV489887
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
EST: gi|5915107|gb|AW052748.1|AW052748
EST:     ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAG                         GAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA
genomic: ACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 42

TAATCTTCTCAAGGGAATACCATTCCTGAAGCCATTTCCCAGTCATTCTAACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAACTGAAAGGCTATATTCGTATCTCGGTTGGGAAACCCGAGCACACTGATG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 63

TAATCTTCTCAAGGGAATACCATTCCTGAAGCCATTTCCCAGTCATTCTAACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAACTGAAAGGCTATATTCGTATCTCGGTTGGGAAACCCGAGCACACTGATG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 49

TAATCTTCTCAAGGGAATACCATTCCTGAAGCCATTTCCCAGTCATTCTAACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAACTGAAAGGCTATATTCGTATCTCGGTTGGGAAACCCGAGCACACTGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 56

TAATCTTCTCAAGGGAATACCATTCCTGAAGCCATTTCCCAGTCATTCTAACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgtttta ... aaaatttcagGAAGACCTTGCGAAGATGGGAGTGATGATCCGCCACTATGACAAGAAGGAACTGAAAGGCTATATTCGTATCTCGGTTGGGAAACCCGAGCACACTGATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAATCTTCTCAAGGGAATACCATTCCTGAAGCCATTTCCCAGTCATTCTAACTTCATTCTCTGCGAGGTCACGTCAGGAAAGGATGCAAAGAAAATAAAGgtttgttttatttattgctgcatgtttgcatttccatcttattcctttgaggtatcagtcacttttattgtgatttaaggtcagaaaatattagtgcttgtttttatgcaggaatgtttggaagagtatgcaatttgcagcattactcacatgttttattgacaaaaatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA