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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gactgtcttgagccttcagatgacgccattcactgtttgctgttagcctctgtttgatacacctgtccgtaggtgctaatgttctgtttttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGA

Basic information

species Zea mays
transcript GRMZM2G029685_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029685_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G43190.1 (Glycine max), 3'ss of exon 3
gactgtcttgagccttcagatgacgccattcactgtttgc---tgttagcctctgtttgatacacctgtccgtaggtgctaatgt-tctgtttttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGA
   | |||      |    ||||    |||   |  |      | || |||    ||  ||     ||| |    |  ||||  | ||| | | |  |   |||||||||||||  ||||||||||| |||||| | ||||| ||||||||  | ||||| || || ||||| || ||||| || ||||||    
---tatctgatatttgagaatgataatatttttttataatgtgtcttggccataattacatcattttgtgcaagtgaactaaaatatctatctattat-atcagAACGGCCTTGACACCAAGGTAGAAAAGTCAAGGAAGCAAATGAAGGAGAGAAAGAATAGAGCTAAGAAGATTCGTGGAGTAAAGAAG----

upper sequence: GRMZM2G029685_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G28060.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------gactgtcttgagccttcagatgacgccattcactgtttgctgttagcctctgttt------gatacacctgt-ccgtag----gtgctaatgtt-ctgtt--tttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGA
                                        ||  |  ||  || ||   |    | ||   ||    || |   | ||| ||      || |||   ||   | |      | || |  |   ||||  | |  | ||||||| || ||||  |||||| | ||||| ||| | || ||||| |||||  | ||||||||||||||||| ||||||||||| ||||||    
gtaatttctctttacttgtttgatagttaagtaaaacttttggttctagtttttagtctagcttactcttggtgctttgattttcactgctttgcgatgaaacaatggtgttgcaatctcatactgaaatgattgttgatgtgattgacagAATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAG----

upper sequence: GRMZM2G029685_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT3G04920.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------------------------------------------------------gactgtcttgagccttcagatga-cgccattcactgtttgctgttagcctctgtttgatacacctgtccgtaggtgctaatgttctgtttttc--gtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGA
                                                                                              ||   |  | |||  |  ||| |    |   |  | | |  | ||   ||  || |  |   | | |   ||  |    ||| | ||| | |   || | ||||| || ||||  || ||| | ||||||||| | || || || |||||| | ||||||||||||||||||||||||||||| ||||||    
gtaaatgctttttccactcttgtttccattgttatatattgctactcacattgacccgtcttaaatcattactcttgctcattactgtttgtctgaaaattataagctatgtgataagtttcggactttatatcgtattgcacttggtgttctctgcatctttatacttaaacatgctttgtctatgtggttggcagAATGGACTTGACACTAAGATTGAGAAGTCAAGGAAACAAATTAAGGAAAGGAAGAACAGGGCGAAGAAAATCCGTGGTGTTAAGAAG----

upper sequence: GRMZM2G029685_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0151g00900.t01 (Vitis vinifera), 3'ss of exon 3
gactgtcttgagccttcagatgacgccattcactgtttgctgttagcct-ctgtttgatacacctgtccgtaggtgctaatgttctgtttttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGA
 ||     ||  |  | ||   ||         | | |    |||   | || || || |||    ||  |   |   |   |      ||   |   ||||| ||  | | ||||||||| || |||||| | ||||| ||||||||| | ||||||||||| |||||  |||| || |||||||||    
-acaacaatgtacacttagtgaacaaggaatcttatcttgctttattttgctattcgaaacatgcttctctttctctgaccatagcaacttgtctgcgcagAATGGATTGGATACCAAGGTGGAAAAGTCAAGGAAGCAAATGAAGGAAAGGAAGAACAGGGCCAAGAAGGTCCGAGGAGTGAAGAAG----

upper sequence: GRMZM2G029685_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------------gactgtcttgagccttcagatgacgccattcactgtttgctgtta-gcctctgtttgatacacctgtccgtaggtgctaatgttctgtttttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGA
                                                             | || |   ||  | |||    |||  ||| ||| | |   |  |   ||||  |      |  |||  ||   ||  | |  |  |  |   ||||| || || ||||||||||| ||||||||  | |||||||| ||||| || |||||| |  ||||||| ||| | ||||||||||||    
gtgagattcatcgagacctgattggttcatccggctctgaggttcttgaaaggtcaaggcatgtt-atttttttgttgaaataatttgctgattggtttggtgtgttcatttgtcaagatctttagtat-tgaggatagtttaatggttatttgcagAATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAG----

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|211011481|gb|FL283787.1|FL283787
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
EST: gi|60397441|gb|DN230257.1|DN230257
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
EST: gi|211008706|gb|FL283775.1|FL283775
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAA
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAA
EST: gi|15079941|gb|BI388886.1|BI388886
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
EST: gi|211011487|gb|FL283793.1|FL283793
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
EST: gi|60355885|gb|DN222858.1|DN222858
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
EST: gi|211014263|gb|FL283805.1|FL283805
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
EST: gi|16926632|gb|BM079700.1|BM079700
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
EST: gi|211008700|gb|FL283769.1|FL283769
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAAC
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAAC
EST: gi|37376305|gb|CF624665.1|CF624665
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctctgtttgatacacctgtccgtaggtgctaatgttctgtttttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGA
                            tgctaat  putative branch site (score: 2)
                                    ttctgtttttcgtc  CT-rich tract
       tttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gactgtcttgagccttcagatgacgccattcactgtttgctgttagcctctgtttgatacacctgtccgtaggtgctaatgttctgtttttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - -gccttca
- - - - - - - - - - - - - cattcac
- - - - - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttctg