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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcacttttcattccaatgaagtgaccccgctgctagcaattttattttttgttgataaaaaccaactatgtatagaccatctatcttcatctcattttctttccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCGTACCGAAATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGT

Basic information

species Zea mays
transcript GRMZM2G132060_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132060_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S98_7V6.1 (Physcomitrella patens), 3'ss of exon 4
gtgcacttttcattccaatgaagtgaccccgctgctagcaattttattttttgttgataaaaaccaactatgtatagaccatctatcttcatctcattttctttccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCGTACCGAAATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGT
          |||  |||      ||      ||  |   ||| |  ||   ||| |            |||     || |||    ||  |    |||   |   || |  |||| ||||||||||||||||||||||||    | ||||| | ||| || |  || || || ||||| || || || ||||| |||| ||| ||||| ||||
--------ggcatcacaa-acttcgatttgtttgtcatagattgtgctt---gtttaagggggttgctcatgcgctaacaatcgtcattggtggtctttgtgtctgaaat--agGTTTGGGATGCAACTGCTGCAGATCCACGTCTTCTTGTTTTTCTGAAAGGTTATCGTAACACAGTTCCCGTTCCAAGGCATTGGTGTCAAAAGCGAAAGT
















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|211162502|gb|FL243921.1|FL243921
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|23357746|gb|BU645395.1|BU645395
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|20811117|gb|BQ295595.1|BQ295595
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|211159306|gb|FL243892.1|FL243892
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAGGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|148930320|gb|EE284721.2|EE284721
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|148936928|gb|EC881083.2|EC881083
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|148974670|gb|EE025472.2|EE025472
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|31359279|gb|CD443636.1|CD443636
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|211159299|gb|FL243885.1|FL243885
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAGGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|148944299|gb|EC889396.2|EC889396
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|32929819|gb|CF034631.1|CF034631
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|148931686|gb|EC874876.2|EC874876
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|5555529|gb|AI881480.1|AI881480
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|22521467|gb|BU080278.1|BU080278
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|91050200|gb|EB160618.1|EB160618
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|211162494|gb|FL243913.1|FL243913
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|21843267|gb|BQ703848.1|BQ703848
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCG-GGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|211159303|gb|FL243889.1|FL243889
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGNATGCA-CTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGC
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGG-ATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGC
EST: gi|211159301|gb|FL243887.1|FL243887
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTG
EST: gi|148931684|gb|EC874873.2|EC874873
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|26557871|gb|CA830106.1|CA830106
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|148966452|gb|EE017460.2|EE017460
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|89761601|gb|DY689546.1|DY689546
EST:     TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|21843287|gb|BQ703868.1|BQ703868
EST:     TGAAGATTGCAGACCTC-AACAGATATGCAACAGACCTGACGTCG-GGAG                         GTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCG
EST: gi|211160900|gb|FL243906.1|FL243906
EST:     TGAAGATTGCAGACCTCAAACAGA-ATGCAACAAACCTGACGTCGTGGAG                         GTCTGGGATGCNACTGCTGCAAATCCAAAAATGCT-GTATTTCTCAAGG
genomic: TGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGG

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: 49 (upstream exon), 43 (downstream exon)
Score: 574

GAAGAAGGACGGAGGCCTATCCAATAAGAAGAAGAAGCTGGAACGCAGGATGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCGTACCGAAATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 310

GAAGAAGGACGGAGGCCTATCCAATAAGAAGAAGAAGCTGGAACGCAGGATGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCGTACCGAAATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 485

GAAGAAGGACGGAGGCCTATCCAATAAGAAGAAGAAGCTGGAACGCAGGATGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCGTACCGAAATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 264

GAAGAAGGACGGAGGCCTATCCAATAAGAAGAAGAAGCTGGAACGCAGGATGAAGATTGCAGACCTCAAACAGATATGCAACAGACCTGACGTCGTGGAGgtgcactttt ... ccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCGTACCGAAATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaccaactatgtatagaccatctatcttcatctcattttctttccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCGTACCGAAATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGT
                   ccatctatcttcatct  CT-rich tract
                                    attttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcacttttcattccaatgaagtgaccccgctgctagcaattttattttttgttgataaaaaccaactatgtatagaccatctatcttcatctcattttctttccaattccagGTCTGGGATGCAACTGCTGCAGATCCAAAATTGCTTGTATATCTCAAGGCGTACCGAAATACAGTACCTGTCCCTAGGCACTGGTCTCAGAAGCGCAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC