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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctaatggtttgtaaggaattggctctaatttctttaagtacacctatgcatttagtatcagtgcattacaattttcattggtttcttatggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAGTTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC

Basic information

species Zea mays
transcript GRMZM2G038126_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 1
ttctaatggtttgtaaggaattggctctaatttctttaagtacacctatgcatttagtat-cagtgcattacaattttcattggtttcttatggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAGTTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC
 ||  ||    || |    |||   | |   |   |  | |  |   || || |    |   |    |||  ||  ||  || | |||| |   | | ||||||||||||||||| ||||||||||| |||||||| |||||||| ||||| |||||  |||| ||||||||| |||||||||||||||||||||||||||
ctcacatatcctggagcttatttattattgctcactgtaatctattcatacagtcgacaaataaaatatt-taacatttttttgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC

upper sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 1
ttctaatggtttgtaaggaattggctctaatttctttaagtacacctatgcatttagtatcagtgcattacaattttcattggtttcttatggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAGTTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC
  |  ||| || |||     |      |  | |||| | |      | |    ||| |  ||     |||     ||     || | | ||  | |  |||| ||||||||||| || ||||| || || ||||| || ||||| || ||| ||||| | || ||||||||  | ||||| || ||||||||||||||||
ggcctatgtttagtatattgtcaaacatgttgtcttgagggttttgttttttattaatggcatgttcttatccccttttcatgtatttgatattttttagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGCGAGGCCGTGGAGCTACCCCTTACGCATCATGAACTATACAAACAAATTGGTATTGATCCTC

upper sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 1
ttctaatggtttgtaaggaattggctctaatttctttaagtacacctatgcatttagtatcagtgcattacaattttcattggtt---tcttatggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAGTTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC
   || |||  ||| |  |  | | | |||||| |     |    || ||  |||| |    |    |    ||   | || | |   | | ||  | |  |||| ||||||||||| || ||||| || || ||||| || ||||| || ||| ||||| | || ||||||||  | ||||| || ||||||||||||||||
aattactggcatgttattatgtag-tataatttatcccctttt--ctttgagtttaattgttgcatgtccttatccccctttgatgtatttgatcttttttagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGTGAGGCTGTGGAGCTACCCCTTACACATCATGAACTATACAAACAAATTGGTATTGATCCTC

upper sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 1
-ttctaatggtttgtaaggaattggctctaatttctttaagtacacctatgcatttagtatcagtgcattacaattttcattggtttcttatggtgtgc-agGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAGTTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC
  | | |  |||||  |    ||   | |||   | ||   || |    ||   ||    |||| |  ||  ||||     |  |||  ||   | |   |||||||||||||||| || || || ||||| ||||| || || || ||||||||||| ||||||||||||||| ||||||| ||||||||||| |||||||
tatttgaatgtttgccatctttttattgtaaacacatttc-taaatggttggggttctggtcagagt-ttgaaattcatggtttttttgtaccttttattagGATATTGGAGGATGTGATATTCAGAAGCAGGAAATCCGTGAAGCTGTTGAGTTACCTTTGACTCATCATGAGCTGTACAAACAGATTGGTATAGATCCTC

upper sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S79_171V6.1 (Physcomitrella patens), 3'ss of exon 1
ttctaatggtttgtaaggaattggctctaatttcttta--agtacacctatgcatttagtatcagtgcattac-aattttcattggtttctt--atggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAGTTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC
    |||  || |    |||||  |  | ||| ||  |   |    | || ||||   ||    ||  | ||  ||||  |  || | | ||   | | ||||||||||| || || || || || || || ||||| ||  |||| || || ||| | ||  | |||||||| ||||| |||||||||||||||||||| || |
--tcaatatttcgctgcgaatt--caatgattcctggactggcttgctta-gcatcgtgttggtgtttactatgaattggcggtgatgtatttggttgagtgcagGATATAGGTGGGTGTGATATTCAGAAACAAGAGATTAGGGAAGCTGTGGAGCTTCCACTTACTCATCACGAGTTATACAAGCAGATTGGTATTGACCCAC

upper sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 1
ttctaatggtttgtaaggaattggctctaatttctttaagtacacctatgcatttagtatcagtgcattacaattttcattggtttcttatggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAGTTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC
            ||||| | ||  ||    ||  | |    || | |  |   |  || |   ||  |   |    |  ||   |  || |    | |||||||||||||| || |||||||| ||||||||||| || ||||| || ||| | ||  |||| || || ||| | ||||||||||||||||| ||||| |
------------gtaagaatttttct----ttcttcttgcgactcttgagggctc-gtgttcttgggtctaagcacttctt---tctttgtttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTATACAAGCAGATTGGTATCGATCCAC

upper sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 1
ttctaatggtttgtaaggaattggctctaatttctttaagtacacctatgcatttagtatcagtgcattacaattttcattggtttcttatggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAGTTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC
            ||||| ||||  || |  |    || |   | | | | | ||  || | |   | |   | |||      |||||||        |||||||||||||| || |||||||| ||||||||||| || ||||| || ||| | ||  |||| || || ||| | ||||||||||||||||| ||||| |
------------gtaagaaattttctttcttactcttgaaggctcgtgttc-ttgggtctaaacacttcttacttt------gtttcttt-------cagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC

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|148947211|gb|EC892559.2|EC892559
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|211138524|gb|FL389537.1|FL389537
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCA
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCA
EST: gi|67017682|gb|CO446431.1|CO446431
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|31355065|gb|CD439422.1|CD439422
EST:     CCTTTATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|211182065|gb|FL377598.1|FL377598
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGC
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGC
EST: gi|78112287|gb|DV530681.1|DV530681
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|60351799|gb|DN218772.1|DN218772
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|148969597|gb|EE020436.2|EE020436
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|148931878|gb|EC877342.2|EC877342
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|211538979|gb|FL382883.1|FL382883
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|32908278|gb|CF013091.1|CF013091
EST:     CAGCATCTCCTTGCTGGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CAGCATCTCCTTGCT-GGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|211348050|gb|FL372962.1|FL372962
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGGTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|32847686|gb|CD987367.1|CD987367
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGTCCAACGTCACCTACACC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|149064643|gb|EE286517.2|EE286517
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTG
EST: gi|149081030|gb|EE170130.2|EE170130
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|31354242|gb|CD438599.1|CD438599
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|148954720|gb|EC900173.2|EC900173
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|38229719|gb|CF920032.1|CF920032
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|148958333|gb|EC904556.2|EC904556
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
EST: gi|89756138|gb|DY686288.1|DY686288
EST:     CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAAC                         GATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG
genomic: CCAGCATCTCCTTGCTGGGATCGTCGGAGAAGCCCAACGTCACCTACAACgtaagtttat ... tggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatgcatttagtatcagtgcattacaattttcattggtttcttatggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAGTTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC
                                      tttcttat  CT-rich tract
                     attacaattttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctaatggtttgtaaggaattggctctaatttctttaagtacacctatgcatttagtatcagtgcattacaattttcattggtttcttatggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAGTTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT