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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatcttgagtcttatttttttcagttcactatgaagatcgattgtgtattctctattcttgtatctaacctgagatgtgtttacctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT

Basic information

species Zea mays
transcript GRMZM2G422581_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G422581_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G29720.1 (Glycine max), 3'ss of exon 8
--------gtgaatcttgagtcttatttttttcagttcac--tatgaagatcgattgtg-tattctctattcttg-------tatctaacctgagatgtgtttaccta--tttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT
         | | | || |  |  |||  |   |  | |   ||||| | |   || || || |    ||            ||  | |  |||    | | |  |    ||||||||  |||||||||| || || || |||||||||||||||||||| |||||||| |  ||    ||  |    ||||||||||||||||||| |      |
gtaattgtttcattatttaaccccattactccaaaattatgttatgatgttttcttttgctagttgtcatgtaaaaggaagataaatgatttgacgcatttcttgcggattttcagATATTGAGATGTGGCCCCCCACCTATGAACAAGGCCATGGCTGCTCACCTTGAAGCCCTTGGATATGCTCCTGAGATGCAGTTCCAGTTCTGATTCTCTT

upper sequence: GRMZM2G422581_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 8
gtgaatcttgagtcttatttttttcagttcactatgaagatcg-attgtgtattctctattcttgtatctaacc-----------tgagatgtgtttaccta----tttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT
|| | | ||   |  |||||    || | | | |  |  ||   ||| | | ||    ||  ||| ||  ||             | ||| ||||||         ||||||||  |||||||||| || || || ||||||||||||||||||||||||||||| |  ||    ||  |    ||||||||||||||||||| |      |
gtaattgtttcat--tatttaacccattactccaaaattatgatattttcttttgctaatcattgcataaaaggaagataaatgattagacgtgtttcttgcggattttcagATATTGAGATGTGGCCCACCACCTATGAACAAGGCCATGGCTGCACACCTTGAAGCCCTTGGATATGCTTCTGAGATGCAGTTCCAGTTCTGATTCTCTT

upper sequence: GRMZM2G422581_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT5G17770.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgaatcttgagtcttattttttt---cagttcactatgaagatcgattgtgtattctctattcttgtatctaacctgagatgtgtttacct----atttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT
 || |    || | | |  ||  |   || |||| | |       ||   | |  | |    |  ||| ||  | || ||    ||| |  |    ||| |||||||| ||||| || || || || ||||||||||||||||||||| ||||||| |  ||    ||| |   ||||||||| |||||||||| | |    |
-tgcaaga-gaatgtaacattgataaacaattcatttttggtgaggagcatatggtttaagatggtgtgtc-gatctaagtatggttcatgtttaaattgcagATCCTAAGATGCGGACCACCGCCAATGAACAAGGCCATGGCTGCAAACCTTGAAGCTCTGGGATACTCTCCGGAGATGCAATTCCAGTTCTGATCTGAAT

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|76288676|gb|DV028244.1|DV028244
EST:     TTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
genomic: CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
EST: gi|60291769|gb|DN190008.1|DN190008
EST:     CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
genomic: CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
EST: gi|19058036|gb|BM736703.1|BM736703
EST:     TAAGGAAATGATCCAATCTCATTGTCCCAGCGCCTGCTGAGGACATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGA
genomic: TAAGGAAATGATCCAATCTCATTGT-CCAGCGCCTGCTGAGGACATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGA
EST: gi|37381869|gb|CF627838.1|CF627838
EST:     CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
genomic: CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
EST: gi|76290843|gb|DV030411.1|DV030411
EST:     CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
genomic: CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
EST: gi|19822090|gb|BQ048114.1|BQ048114
EST:     CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
genomic: CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
EST: gi|211184106|gb|FL465367.1|FL465367
EST:     CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
genomic: CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
EST: gi|211135586|gb|FL028680.1|FL028680
EST:     CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
genomic: CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
EST: gi|19822109|gb|BQ048133.1|BQ048133
EST:     GATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
genomic: GATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
EST: gi|88751068|gb|DY535209.1|DY535209
EST:     CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
genomic: CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
EST: gi|166680168|gb|EG164832.1|EG164832
EST:     GGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACAATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGC
genomic: GGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGAC-ATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGC
EST: gi|50331967|gb|CO527093.1|CO527093
EST:     CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
genomic: CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
EST: gi|26455934|gb|CA827517.1|CA827517
EST:     CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
genomic: CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
EST: gi|78117349|gb|DV535736.1|DV535736
EST:     CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
genomic: CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
EST: gi|19769752|gb|BQ034473.1|BQ034473
EST:     CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
genomic: CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
EST: gi|76288677|gb|DV028245.1|DV028245
EST:     CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAG                         ATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT
genomic: CTAAGGAAATGATCCAATCTCATTGTCCAGCGCCTGCTGAGGACATTCAGgtgaatcttg ... cctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgattgtgtattctctattcttgtatctaacctgagatgtgtttacctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT
                        atctaac  putative branch site (score: 2)
                                             cctatttc  putative PPT
               tattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatcttgagtcttatttttttcagttcactatgaagatcgattgtgtattctctattcttgtatctaacctgagatgtgtttacctatttcagATCCTGAGATGTGGTCCTCCTCCGATGAACAAGGCCATGGCTGCACACCTTGACGAGCTCAACTACACAAAGGAGATGCAGTTCCAGTTCTAAGCAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA