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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGCTCTCGATTGATGACATGGCAGGAGGAACATTCACTATCTCCAATGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctactaaacatttatcagttgcaacacatttgtagcatgcagatgtttatattgatctgaaacatgatctatgtgaaatgcag

Basic information

species Zea mays
transcript GRMZM5G807639_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G807639_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 12
GGCGCTCTCGATTGATGACATGGCAGGAGGAACATTCACTATCTCCAATGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctactaaacatttatcagttgcaaca--catttgtagcatgcagatgtttatattgatctgaaaca-tg-atctatgtgaaatgcag
||| ||||| |||||||| |||||||||||||||||||| ||||| || |||||||| || ||||||||  |||||||||||||||||||||||||||||||  ||  |  |  |||  || |||||| |         |  | |  ||| || ||  | |||||| ||| || || ||| |  |||||||
GGCACTCTCAATTGATGAGATGGCAGGAGGAACATTCACCATCTCTAACGGTGGTGTTTACGGAAGCCTTATCAGCACACCTATCATCAACCCCCCACAGgtc-ctttttcatttttgccacttgcaaaaattgccctcactaggttgatattcat--tcatctgacacaatgtatatatatctaatgcag

upper sequence: GRMZM5G807639_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT5G55070.1 (Arabidopsis thaliana), 5'ss of exon 14
GGCGCTCTCGATTGATGACATGGCAGGAGGAACATTCACTATCTCCAATGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctactaaacatttatca-gttgcaacacatttgtagcatgcagatgtttatattgat-----ctgaaacatg-atctatgtgaaatgcag
  |  | || || ||||| |||||||||||| |||||||  | || |||||||||||||||||||| ||  | ||||| |||||||||||||| || |||||  | | |  |   ||   |   |  ||  || |   || | |  | | |||   ||| |     || |  ||   |  | | | | | | ||
AACCATATCAATCGATGAGATGGCAGGAGGATCATTCACAGTATCAAATGGTGGTGTCTATGGAAGTCTTATAAGCACTCCTATCATCAACCCTCCTCAGgtt-cgattcgatccttgcaatactaaaaaccaatcaaagaaaggtgtttttttgtttgtttgttactaatgcaaataaatctatcatacgtag

upper sequence: GRMZM5G807639_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv19s0090g00750.t01 (Vitis vinifera), 5'ss of exon 9
GGCGCTCTCGATTGATGACATGGCAGGAGGAACATTCACTATCTCCAATGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctactaaacatttatcagttgcaacacatttgtagcatgcagatgtt--tatattgatctgaaa--catgatctatgtgaaatgcag-------------------------------------------------------------------------------------------------
  |  | || |||||||| ||||| |||||  ||||||| || |||||||||||||| |||||||||||  | || || || |||||||| ||||| |||||      | ||   ||  | | ||||| |  ||   |   ||  |||  |  | || | ||||  ||   ||  | | |     ||||                                                                                                   
AACCATATCAATTGATGAGATGGCTGGAGGTTCATTCACAATATCCAATGGTGGTGTGTATGGAAGCCTTTTGAGTACTCCCATCATCAATCCCCCTCAGgt------tcaaggctttactgatgcaataagttgaaattttggtgattctcttttaataatctagaagatatactttttccttcatgccctgatgataaattgtcataaaaccctctggttatccatatcagtagattcctttcgtaattaaacagagaacctcacacattctaacatctttgacag

upper sequence: GRMZM5G807639_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv10s0116g01480.t01 (Vitis vinifera), 5'ss of exon 15
GGCGCTCTCGATTGATGACATGGCAGGAGGAACATTCACTATCTCCAATGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgta----gct------actaaacatttatca-gttgcaacacatttgtagcatgcagatgtttatattgatctgaaacatgatctatgtgaaatgcag---
  |  | || || ||||| ||||| || ||  ||||||| || ||||||||||||||||||||||||||  | || || || ||||||||||| || ||||||    |||      || |  | | ||||  |||   | |  |||      |     |||| | ||   |||     ||  ||||  |||| ||      
CACCATATCTATCGATGAGATGGCTGGTGGCTCATTCACAATATCCAATGGTGGTGTCTATGGAAGCCTGTTGAGTACCCCAATCATCAACCCTCCCCAGgtaagaagcttcatagaccattcttctatcctgttaggataattttaggatttcttactgttcacatatttcttttgaattgtcta-atgaattgtgaaac

upper sequence: GRMZM5G807639_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S2_220V6.1 (Physcomitrella patens), 5'ss of exon 8
GGCGCTCTCGATTGATGACATGGCAGGAGGAACATTCACTATCTCCAATGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctactaaacatttatcagttgcaacacatttgtagcatgcagatgtttatattgatctgaaacatgatctatgtg-aaatgcag-----------------
|    |  | |||||||| ||||| |||||||| || |||||||| ||||||||||| ||||| || ||| | ||||| ||||| |||||||| || ||   || |  | ||  | | ||     |||| | |||| |  || |   ||||   ||| |   | | |   | | |  || |||||                    
GAGCATAACCATTGATGATATGGCGGGAGGAACTTTTACTATCTCTAATGGTGGTGTTTATGGGAGTCTCATAAGCACTCCTATTATCAACCCTCCTCA---Agttggtcaatttctttct-cgacaactcttttg-aatatcctcttgttataattaactggcagcgaaaccgaaatgcaaatgtttatttccgaaattccagg

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|93017174|gb|EB642694.1|EB642694
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|6918669|gb|AW400199.1|AW400199
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|32935625|gb|CF040437.1|CF040437
EST:     GTAGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|211354774|gb|FL462364.1|FL462364
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|16925492|gb|BM078560.1|BM078560
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|5871687|gb|AW018158.1|AW018158
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|60343714|gb|DN210687.1|DN210687
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|6020821|gb|AW065749.1|AW065749
EST:     GTGGTGTCTATGGAAGCCTNCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGNTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|16919656|gb|BM074297.1|BM074297
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|32866729|gb|CF006411.1|CF006411
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|16926010|gb|BM079078.1|BM079078
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|30306816|gb|CD001489.1|CD001489
EST:     CTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: CTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|60349623|gb|DN216596.1|DN216596
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|6918383|gb|AW399913.1|AW399913
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|211104574|gb|FL031920.1|FL031920
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
EST: gi|60399105|gb|DN231919.1|DN231919
EST:     GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAG                         TCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT
genomic: GTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctacta ... tgaaatgcagTCGTCAATTCTGGGGATGCATTCCATTGTGCAACGCCCTGTGGTTGTGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGCTCTCGATTGATGACATGGCAGGAGGAACATTCACTATCTCCAATGGTGGTGTCTATGGAAGCCTCCTCAGCACACCTATCATCAACCCCCCACAGgtagctactaaacatttatcagttgcaacacatttgtagcatgcagatgtttatattgatctgaaacatgatctatgtgaaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC