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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatcgcctttcaaccaaagatcatgccttggcaatagatgtgactgtttttggtctctgacctgtcgtcttttgtttggtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGAATATCAAATGTGATTAAATCCCTGCTGCTTAAGCTAGCAACAGAAAAAT

Basic information

species Zea mays
transcript GRMZM2G420310_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 11
gtaagatcgcc-tttcaaccaaagatcatgccttggcaatagatgtgactgtttttggtctctgacctgtcgtcttttgtttggtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGAATATCAAATGTGATTAAATCCCTGCTGCTTAAGCTA-GCAACAGAAAAAT
||||||||    |||| || |       |   |  |  | |  | |  |  | |   || | ||   || | ||| ||  |||| ||||| ||| ||||||||||||||||||||||| |||||||| |||||||||||||| || |||||||||||||| ||    || | ||     |   | ||||  |  
gtaagatcttaatttctactagtaccttttaatccgtgacactt-tatcattatgatgtttttgttttgacatctgtt--ttggcgattc-agGTGCTATTGGCTATCTAGGGTCAACTCTTTTTGTGAGGAGAATCTACAGAAACATCAAATGTGATTAGATGATCGCAGTTTGGAAGACATAGCAGATCAC-
















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|8103138|gb|AW927796.1|AW927796
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|21891547|gb|BQ744760.1|BQ744760
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|94476144|gb|EB705102.1|EB705102
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|31358755|gb|CD443112.1|CD443112
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|14717686|gb|BI245336.1|BI245336
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|78022089|gb|DV490476.1|DV490476
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|15100489|gb|BI396280.1|BI396280
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|60353188|gb|DN220161.1|DN220161
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|7844572|gb|AW787794.1|AW787794
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|60354201|gb|DN221174.1|DN221174
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|60346086|gb|DN213059.1|DN213059
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|6022591|gb|AW067403.1|AW067403
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|60395872|gb|DN228742.1|DN228742
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|83278727|gb|DV942735.1|DV942735
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|211305971|gb|FL442632.1|FL442632
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|13515787|gb|BG518063.1|BG518063
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|211305970|gb|FL442631.1|FL442631
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|16379626|gb|BI993061.1|BI993061
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|4647025|gb|AI622100.1|AI622100
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|4647026|gb|AI622101.1|AI622101
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|24766392|gb|CA401546.1|CA401546
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|211510341|gb|FL458348.1|FL458348
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|71773864|gb|DR971755.1|DR971755
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|60397922|gb|DN230738.1|DN230738
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
EST: gi|15079859|gb|BI388859.1|BI388859
EST:     CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTG                         GAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA
genomic: CTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGA

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), 47 (downstream exon)
Score: 204

TACTACTACCATGTGAAGACAAAGATGTCAGGCTTCTTCCAGACAAGTTTCTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGAATATCAAATGTGATTAAATCCCTGCTGCTTAAGCTAGCAACAGAAAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

TACTACTACCATGTGAAGACAAAGATGTCAGGCTTCTTCCAGACAAGTTTCTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGAATATCAAATGTGATTAAATCCCTGCTGCTTAAGCTAGCAACAGAAAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 378

TACTACTACCATGTGAAGACAAAGATGTCAGGCTTCTTCCAGACAAGTTTCTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGAATATCAAATGTGATTAAATCCCTGCTGCTTAAGCTAGCAACAGAAAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 321

TACTACTACCATGTGAAGACAAAGATGTCAGGCTTCTTCCAGACAAGTTTCTATTTCGGCTACACGCTGATGTTCTGCCTTGGCCTAGGCATACTTTGTGgtaagatcgc ... gtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGAATATCAAATGTGATTAAATCCCTGCTGCTTAAGCTAGCAACAGAAAAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagatgtgactgtttttggtctctgacctgtcgtcttttgtttggtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGAATATCAAATGTGATTAAATCCCTGCTGCTTAAGCTAGCAACAGAAAAAT
                     ctctgac  putative branch site (score: 321)
                                    ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatcgcctttcaaccaaagatcatgccttggcaatagatgtgactgtttttggtctctgacctgtcgtcttttgtttggtgattccagGAGCTATTGGCTATCTAGGGTCAACCCTTTTTGTAAGGAGAATCTACAGGAATATCAAATGTGATTAAATCCCTGCTGCTTAAGCTAGCAACAGAAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT