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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatcaacgacgatattttggcatccttcatgtactaataatggttccttggtttcgttataagttccatccattgatccgttttatcgtgttcgtcgtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC

Basic information

species Zea mays
transcript GRMZM2G155384_T01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155384_T01 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 21
------gtatatatcaacgacgatattttggcatccttcatgtactaataatggttccttggtttcgttataagttccatccattgatccgttttatcgtgttcgtcgtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC
        ||| ||| || | |||  |||   | |  |  |  | |  |  ||  | | |||||    ||||   | | | |||  ||       ||  ||   ||  |||||| |||||||| || || ||||| ||||| || ||||| |||||||| || |||||||||||||| ||  | ||||| || |||||
gtaagttaataaatccacaatgatccttttaaacctgtgctccattc-tgttg--tacctggttg---tatataatgcgtacatatattgacaaaattttgcatgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTCTCTCCATACCATTCTGACCGGTTTCTACTTTCCCC
















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|32929670|gb|CF034482.1|CF034482
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|32929670|gb|CF034482.1|CF034482
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|18384394|gb|BM417593.1|BM417593
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTCGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|18384394|gb|BM417593.1|BM417593
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTCGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|32926108|gb|CF030920.1|CF030920
EST:     AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTAG                         AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
genomic: AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTG-TAAgtatatatca ... gtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
EST: gi|32841969|gb|CD981650.1|CD981650
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|32841969|gb|CD981650.1|CD981650
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|211100368|gb|FL070846.1|FL070846
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|211100368|gb|FL070846.1|FL070846
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|32926755|gb|CF031567.1|CF031567
EST:     CAATCTTTCAAGGTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|32926755|gb|CF031567.1|CF031567
EST:     CAATCTTTCAAGGTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|211100372|gb|FL070850.1|FL070850
EST:     AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTAG                         AATTGCCCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTTTCCC
genomic: AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTG-TAAgtatatatca ... gtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
EST: gi|32925375|gb|CF030187.1|CF030187
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|32925375|gb|CF030187.1|CF030187
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|32867559|gb|CF007241.1|CF007241
EST:     AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTAG                         AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
genomic: AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTG-TAAgtatatatca ... gtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
EST: gi|32925086|gb|CF029898.1|CF029898
EST:     AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTAG                         AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
genomic: AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTG-TAAgtatatatca ... gtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
EST: gi|211100371|gb|FL070849.1|FL070849
EST:     AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTAG                         AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCYTTCTC
genomic: AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTG-TAAgtatatatca ... gtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
EST: gi|32925553|gb|CF030365.1|CF030365
EST:     AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTAG                         AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
genomic: AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTG-TAAgtatatatca ... gtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
EST: gi|32926620|gb|CF031432.1|CF031432
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|32926620|gb|CF031432.1|CF031432
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|211100370|gb|FL070848.1|FL070848
EST:     ATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTAG                         AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
genomic: ATTACTACAAAGAAGCTGCTCATCTGTTTTGTG-TAAgtatatatca ... gtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
EST: gi|32849654|gb|CD989335.1|CD989335
EST:     AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTAG                         AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
genomic: AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTG-TAAgtatatatca ... gtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
EST: gi|32908274|gb|CF013087.1|CF013087
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|32908274|gb|CF013087.1|CF013087
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|32928954|gb|CF033766.1|CF033766
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|32928954|gb|CF033766.1|CF033766
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|32841970|gb|CD981651.1|CD981651
EST:     AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTAG                         AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
genomic: AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTG-TAAgtatatatca ... gtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
EST: gi|32925292|gb|CF030104.1|CF030104
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|32925292|gb|CF030104.1|CF030104
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|32928817|gb|CF033629.1|CF033629
EST:     AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTAG                         AATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
genomic: AATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTG-TAAgtatatatca ... gtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTC
EST: gi|32925632|gb|CF030444.1|CF030444
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-
EST: gi|32925632|gb|CF030444.1|CF030444
EST:     CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTTA                         G
genomic: CAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttag-

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: 260

GGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGGCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

GGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGGCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

GGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGGCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

GGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGGCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCTGCTCATCTGTTTTGTGTAAgtatatatca ... gtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgttataagttccatccattgatccgttttatcgtgttcgtcgtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC
                   cattgat  putative branch site (score: 222)
     ttataagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatatcaacgacgatattttggcatccttcatgtactaataatggttccttggtttcgttataagttccatccattgatccgttttatcgtgttcgtcgtcaggttagAATTGCCCAGGGCCTTGTCCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCATACCATTCCGATAGATTTCTCCTCTCCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC