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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgctccacttattcatgttgtttaatattatcctttattcatattgtttgcctttttatgagtctctcagcttttattttatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG

Basic information

species Zea mays
transcript GRMZM2G135283_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 10
gtctgctccactt---attcatgttgtttaatattatcctttattcatattgtttgcctttttatgagtctctcagcttttattttatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG
|||||   |||||   || | || ||||| ||||| |   |   ||| ||||||||||||| | |  | |||| |       || ||  || |||||||||||||| || ||||||||||| |||||||||||||| ||||| ||||| |||||||| |||
gtctgtagcacttctgatccctgatgttttatatttta--tagatcacattgtttgcctttgtcttggactctaaaaggactttctaacttccagGCAACTACTCCGGAGTACAGAGCTTATCAAGAGCAAGTTATGAGTAACTGTGCAAAATTTGCACAG

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv00s0211g00090.t01 (Vitis vinifera), 3'ss of exon 2
------gtctgctcc----acttattcatgttgtttaatattatcctttattcatattgtttgcctttttatgagtctctcagcttttattttatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG
       | ||||      || || |||| || | | | ||        | |    ||     | | |   | |   |||||  | || |||   |   ||||| |||||||||||||||| |||||| ||||| |||||| ||  ||||||| | || |||||  ||
atgaaattttgcttttaaaacatagtcattttttatgaaatataaaggcaattggtttaaaaacttatcattcatattctca--tattctttacaaacgcagGCTACTACTCCAGAATACAAAGCTTATCAAGAACAAGTTCTCTCTAATTGTTCAAAGTTTGCAGAG

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 3'ss of exon 10
gtctgctccacttattcatgttgtttaatattatcctttattcatattgtttgcctttttatgagtctctcagcttttattttatattt----------cagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG
 | ||      ||  |  |      || |  | |   | |   |||  | |      ||||  |   | |||    |  | | |||||           ||||| |||||||||||||||| |||||| ||||| |||||| ||  ||||||| | || |||||  ||
-tatgaaat-tttgcttttaaaacatagtcctttttatgaaatataaaggtaattgctttaaaaacttatcattcatattctcatattctttacaaatgcagGCTACTACTCCAGAATACAAAGCTTATCAAGAACAAGTTCTCTCTAATTGTTCAAAGTTTGCAGAG

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 10
-----gtctgctccacttattcatgttgtttaatattatcctttattcatattg-tttgcctttttatgagtc-tctcagcttttattttatattt-cagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG
        |   |   | |  |||  |  ||  ||| |    | |     |||| |||      |||| | || | |   ||| |  |||| |  | ||||| |||||| ||||||||| |||||| |||||||||||| ||  ||||||| | || |||||  ||
tatgaaattttgcttttaaaacatagtcctttttatgaaatataaaggcaattgctttaaaaacttatcattcatattctcttattctttacaaatgcagGCTACTACTTCAGAATACAAAGCTTATCAAGAGCAAGTTCTCTCTAATTGTTCAAAGTTTGCAGAG

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|148973318|gb|EE024403.2|EE024403
EST:     CCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAG                         GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
genomic: CCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctcca ... tatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
EST: gi|67042253|gb|CO468508.1|CO468508
EST:     GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAG                         GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
genomic: GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctcca ... tatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
EST: gi|6194529|gb|AW146633.1|AW146633
EST:     GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAG                         GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
genomic: GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctcca ... tatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
EST: gi|71299009|gb|DR785497.1|DR785497
EST:     GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAG                         GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
genomic: GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctcca ... tatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
EST: gi|60354435|gb|DN221408.1|DN221408
EST:     ACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAG                         GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
genomic: ACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctcca ... tatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
EST: gi|60343439|gb|DN210412.1|DN210412
EST:     CCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAG                         GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
genomic: CCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctcca ... tatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
EST: gi|40336482|gb|CK370552.1|CK370552
EST:     GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAG                         GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
genomic: GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctcca ... tatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
EST: gi|6102053|gb|AW126523.1|AW126523
EST:     TAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAG                         GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
genomic: TAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctcca ... tatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
EST: gi|67013913|gb|CO442662.1|CO442662
EST:     GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAG                         GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
genomic: GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctcca ... tatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
EST: gi|37393418|gb|CF633973.1|CF633973
EST:     GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAG                         GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
genomic: GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctcca ... tatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
EST: gi|60397906|gb|DN230722.1|DN230722
EST:     GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAG                         GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
genomic: GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctcca ... tatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
EST: gi|14204327|gb|BG838004.1|BG838004
EST:     GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAG                         GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
genomic: GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctcca ... tatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
EST: gi|60351519|gb|DN218492.1|DN218492
EST:     GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAG                         GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
genomic: GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctcca ... tatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
EST: gi|67024112|gb|CO452861.1|CO452861
EST:     GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAG                         GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
genomic: GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctcca ... tatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
EST: gi|60349820|gb|DN216793.1|DN216793
EST:     GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAG                         GCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT
genomic: GTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgctcca ... tatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattcatattgtttgcctttttatgagtctctcagcttttattttatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG
                                    cttttatttt  CT-rich tract
                                     ttttattttatatttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgctccacttattcatgttgtttaatattatcctttattcatattgtttgcctttttatgagtctctcagcttttattttatatttcagGCAACTACTCCAGAATACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG