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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtatttctataatcgtgcagttaactgttgattcaggtacacaaataataccttctttttcagtgcttatttagattaagcataccattccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCTGAAAGCCGCCAATTGCGTGCTGCCCTTGCTGAAGATTCTGGACTTGAAT

Basic information

species Zea mays
transcript GRMZM2G170595_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170595_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g47940.1 (Oryza sativa), 3'ss of exon 2
------------ggtatttctataatcgtgcagttaactgttgattcag-gtacacaaataataccttctttttcagtgcttatttagattaagcataccattccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCTGAAAGCCGCCAATTGCGTGCTGCCCTTGCTGAAGATTCTGGACTTGAAT
            | | ||| ||| | | | |      |||     |||  ||||| || | ||||||||| |          || ||    | ||||| |  |   | ||||||| |||  |||| |||| | | | ||||| ||||||||||||||||||||||||||||| || ||||||||||| ||||||||||||||||| |||||||
gaaaatttaacagatctttgtatgagcatacgaagggctggattctcattgtacataatttataccttctctcc--------atcta----atgcatatctcttt-tatacagGTAGCTAAAGCATTAGGAAATTTGAAGTTTCCCTATGTGTACCCTGATCCTGAAAGCCGTCAGTTGCGTGCTGCTCTTGCTGAAGATTCTGGTCTTGAAT
















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|71437833|gb|DR818883.1|DR818883
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|22489861|gb|BU049784.1|BU049784
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|78078617|gb|DV507029.1|DV507029
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|148974572|gb|EE025361.2|EE025361
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|87153226|gb|DY398015.1|DY398015
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|91048897|gb|EB159315.1|EB159315
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|148963664|gb|EE014723.2|EE014723
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|148932895|gb|EE285676.2|EE285676
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|78079657|gb|DV508069.1|DV508069
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|19822775|gb|BQ048799.1|BQ048799
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|211221376|gb|FL266596.1|FL266596
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|89756009|gb|DY686211.1|DY686211
EST:     ACATAATCAAGTTGGATGCATATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|148932277|gb|EC875831.2|EC875831
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|211221377|gb|FL266597.1|FL266597
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|76289509|gb|DV029077.1|DV029077
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|71332195|gb|DR803018.1|DR803018
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|149109171|gb|EE190055.2|EE190055
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|211221375|gb|FL266595.1|FL266595
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|71328633|gb|DR800987.1|DR800987
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|211221367|gb|FL266587.1|FL266587
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
EST: gi|149111871|gb|EE191026.2|EE191026
EST:     ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG                         GTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT
genomic: ACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCT

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), 49 (downstream exon)
Score: 117

GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCTGAAAGCCGCCAATTGCGTGCTGCCCTTGCTGAAGATTCTGGACTTGAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCTGAAAGCCGCCAATTGCGTGCTGCCCTTGCTGAAGATTCTGGACTTGAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 115

GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCTGAAAGCCGCCAATTGCGTGCTGCCCTTGCTGAAGATTCTGGACTTGAAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 113

GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAGgtgagctcta ... ccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCTGAAAGCCGCCAATTGCGTGCTGCCCTTGCTGAAGATTCTGGACTTGAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataataccttctttttcagtgcttatttagattaagcataccattccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCTGAAAGCCGCCAATTGCGTGCTGCCCTTGCTGAAGATTCTGGACTTGAAT
                                           ttccatct  CT-rich tract
                      ttatttagattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtatttctataatcgtgcagttaactgttgattcaggtacacaaataataccttctttttcagtgcttatttagattaagcataccattccatctacagGTCGCTGCAGCACTAGGTAGTCTCAAGTTCCCCTATGTGTACCCTGATCCTGAAAGCCGCCAATTGCGTGCTGCCCTTGCTGAAGATTCTGGACTTGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - cgtgcag
- - - - - - - - - - - - - tgttgat
- - - - - - - - - - - - - - - - - - - -acacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatacc