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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcagaatttaattcagttcaatacaaattaagatcctcggaagttttcggtcccataaccccattagcatcaagtggatcatgttgcttttcgctgctaatctgagttatcgtttagtttgcagATTATACTTTATGACACTCCTGGTGTTATTAAAAAGGAGATGCATAAGCTGGACAGTATGATGATGAAGAATGTTAGGAGCGCTATCGGCAGTGCGGACT

Basic information

species Zea mays
transcript GRMZM2G158024_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158024_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g49220.2 (Oryza sativa), 3'ss of exon 2
gtatcagaatttaattcagttcaatacaaattaagatcctcggaagttttcggtcccataaccccattagcatcaagtggatcatgttg-cttttcgctgctaatctgagttatcgtttagtttgcagATTATACTTTATGACACTCCTGGTGTTATTAAAAAGGAGATGCATAAGCTGGACAGTATGATGATGAAGAATGTTAGGAGCGCTATCGGCAGTGCGGACT
                        ||  |  |   |   ||  ||| ||| ||    |||  |  || |     ||| ||   |||||   || || |||||||||||||||||| |||||||||||||| |||||||||||||| || ||||| || |||||||| ||||||||||| ||||  ||||||||||||||||||||||| ||  | ||||||       
-----------------------gtatcaccttttagtttctaaagctttaggatt-atagact-atga-----aagggggaaatgttaatttctcactgctaatctgagttatcatttagTTTGCAGATAATACTTTATGACACGCCAGGTGTCATCAAAAAGGAAATGCATAAGCTAGACACAATGATGATGAAGAATGTTAGGAGTGCCGTTGGCAGT-------

upper sequence: GRMZM2G158024_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g49220.1 (Oryza sativa), 3'ss of exon 2
gtatcagaatttaattcagttcaatacaaattaagatcctcggaagttttcggtcccataaccccattagcatcaagtggatcatgttg-cttttcgctgctaatctgagttatcgtttagtttgcagATTATACTTTATGACACTCCTGGTGTTATTAAAAAGGAGATGCATAAGCTGGACAGTATGATGATGAAGAATGTTAGGAGCGCTATCGGCAGTGCGGACT
                        ||  |  |   |   ||  ||| ||| ||    |||  |  || |     ||| ||   |||||   || || |||||||||||||||||| |||||||||||||| |||||||||||||| || ||||| || |||||||| ||||||||||| ||||  ||||||||||||||||||||||| ||  | |||||||| || |
-----------------------gtatcaccttttagtttctaaagctttaggatt-atagact-atga-----aagggggaaatgttaatttctcactgctaatctgagttatcatttagtttgcagATAATACTTTATGACACGCCAGGTGTCATCAAAAAGGAAATGCATAAGCTAGACACAATGATGATGAAGAATGTTAGGAGTGCCGTTGGCAGTGCAGATT

upper sequence: GRMZM2G158024_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G24870.1 (Glycine max), 3'ss of exon 2
gtatcagaatttaattcagttcaatacaaattaagatcctcggaagttttcggtcccataaccccattagcatcaagtggatcatgttgcttttcgctgctaatctga-gttatcgtttagtttgcagATTATACTTTATGACACTCCTGGTGTTATTAAAAAGGAGATGCATAAGCTGGACAGTATGATGATGAAGAATGTTAGGAGCGCTATCGGCAGTGCGGACT
                      || |||| || |  | ||      ||||| ||   ||||     | |   | || |     |  ||  |    |      |  |||   | | |  |   |||||||| |||||||||||||| ||||||||| |  | ||||| |||||   | | |||   ||||||||||| || ||| | || |||   |  | ||| ||||
----------------------aaaacaactttaagtact------ttttcagttgaataaaattttaatactgaattttgctaaattaatggatgtacaacagATGATACTTTTGAATCTCTTGCAGATGATACTTTATGACACACCTGGTGTTCTACAGAAGGAAATGCACTTGTTAGACTCAATGATGATGAAAAACGTTCGCAGTGCTGCAGTTAATGCTGACT

upper sequence: GRMZM2G158024_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0023g02120.t01 (Vitis vinifera), 3'ss of exon 2
gtatcagaatttaattcagttcaatacaaattaagatcctcggaagttttcggtcccataaccccattagcatcaagtggatcatgttgcttttcgctgctaatctgagttatcgtttagtttgcagATTATACTTTATGACACTCCTGGTGTTATTAAAAAGGAGATGCATAAGCTGGACAGTATGATGATGAAGAATGTTAGGAGCGCTATCGGCAGTGCGGACT
                       | | | || || || | |  ||      |    || |  | |||    |   | |     ||   ||| ||     |  |  |||  |   |||| | ||| |||| |||||||||||||| |||||||||||| | ||| | ||||| ||| |||||   |||||||||||||||||  | || |||| |   | ||||||||
-----------------------aaatacataaacatacac--aaccccatgccttcacacacacatataaaagtaatatgctattaagctcttaaaaacgca--tgaacttatgttttgcttgtagATGATACTTTATGACACACCTGGTGTTATTGAGAAGAAAATGCACAAGTTGGACTCCATGATGATGAAGAATGTCCGCAGTGCTACCATTAATGCGGACT

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|211496169|gb|FL037710.1|FL037710
EST:     AACGACAAGACATCGCATTCNTTGGTATATGTTCTGAACCAGAGTACCAG                         ATTATACTTTATGACACGTCCTGGTGTTATTAAAAAGGAGATGCATAAGCT
genomic: AACGACAAGACATCGCATTC-TTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcagATTATACTTTATGACAC-TCCTGGTGTTATTAAAAAGGAGATGCATAAGCT
EST: gi|211496170|gb|FL037711.1|FL037711
EST:     AAACGACAAGACATCGCATTCTTGGTATATGTTCTGGACCAGAGTACCAG                         ATTATACTTTTTGACACTCCTGGTGTTTATTAAAAAGGAGATGCATAAGCT
genomic: AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcagATTATACTTTATGACACTCCTGGTGTT-ATTAAAAAGGAGATGCATAAGCT
EST: gi|149086134|gb|EE175674.2|EE175674
EST:     AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAG                         ATTATACTTTATGACACTCCTGGTGTTATTAAAAAGGAGATGCATAAGCTG
genomic: AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcagATTATACTTTATGACACTCCTGGTGTTATTAAAAAGGAGATGCATAAGCTG
EST: gi|76287840|gb|DV027408.1|DV027408
EST:     AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAG                         T
genomic: AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcag-
EST: gi|76287840|gb|DV027408.1|DV027408
EST:     AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAG                         T
genomic: AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcag-
EST: gi|76287840|gb|DV027408.1|DV027408
EST:     AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAG                         T
genomic: AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcag-
EST: gi|76287840|gb|DV027408.1|DV027408
EST:     AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAG                         T
genomic: AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcag-
EST: gi|76287840|gb|DV027408.1|DV027408
EST:     AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAG                         T
genomic: AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcag-
EST: gi|76287840|gb|DV027408.1|DV027408
EST:     AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAG                         T
genomic: AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcag-
EST: gi|74240633|gb|DT648547.1|DT648547
EST:     AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAG                         ATTATACTTTATGACACTCCCGGTGTTATTAAAAAGGAGATGCATAAGCTG
genomic: AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcagATTATACTTTATGACACTCCTGGTGTTATTAAAAAGGAGATGCATAAGCTG
EST: gi|211496165|gb|FL037706.1|FL037706
EST:     AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAG                         T
genomic: AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcag-
EST: gi|211496165|gb|FL037706.1|FL037706
EST:     AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAG                         T
genomic: AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcag-
EST: gi|211496165|gb|FL037706.1|FL037706
EST:     AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAG                         T
genomic: AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcag-
EST: gi|211496165|gb|FL037706.1|FL037706
EST:     AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAG                         T
genomic: AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcag-
EST: gi|211496165|gb|FL037706.1|FL037706
EST:     AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAG                         T
genomic: AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcag-
EST: gi|211496165|gb|FL037706.1|FL037706
EST:     AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAG                         T
genomic: AAACGACAAGACATCGCATTCTTGGTATATGTTCTGAACCAGAGTACCAGgtatcagaat ... tagtttgcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaagtggatcatgttgcttttcgctgctaatctgagttatcgtttagtttgcagATTATACTTTATGACACTCCTGGTGTTATTAAAAAGGAGATGCATAAGCTGGACAGTATGATGATGAAGAATGTTAGGAGCGCTATCGGCAGTGCGGACT
                         tgctaat  putative branch site (score: 2)
                                           tttagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcagaatttaattcagttcaatacaaattaagatcctcggaagttttcggtcccataaccccattagcatcaagtggatcatgttgcttttcgctgctaatctgagttatcgtttagtttgcagATTATACTTTATGACACTCCTGGTGTTATTAAAAAGGAGATGCATAAGCTGGACAGTATGATGATGAAGAATGTTAGGAGCGCTATCGGCAGTGCGGACT

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