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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gactgtcttgagccttcagatgacgccattcactgtttgctgttagcctctgtttgatacacctgtccgtaggtgctaatgttctgtttttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG

Basic information

species Zea mays
transcript GRMZM2G029685_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029685_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G43190.1 (Glycine max), 3'ss of exon 3
gactgtcttgagccttcagatgacgccattcactgtttgc---tgttagcctctgtttgatacacctgtccgtaggtgctaatgt-tctgtttttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG
   | |||      |    ||||    |||   |  |      | || |||    ||  ||     ||| |    |  ||||  | ||| | | |  |   |||||||||||||  ||||||||||| |||||| | ||||| ||||||||  | ||||| || || ||||| || ||||| || ||||||
---tatctgatatttgagaatgataatatttttttataatgtgtcttggccataattacatcattttgtgcaagtgaactaaaatatctatctattat-atcagAACGGCCTTGACACCAAGGTAGAAAAGTCAAGGAAGCAAATGAAGGAGAGAAAGAATAGAGCTAAGAAGATTCGTGGAGTAAAGAAG

upper sequence: GRMZM2G029685_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G28060.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------gactgtcttgagccttcagatgacgccattcactgtttgctgttagcctctgttt------gatacacctgt-ccgtag----gtgctaatgtt-ctgtt--tttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG
                                        ||  |  ||  || ||   |    | ||   ||    || |   | ||| ||      || |||   ||   | |      | || |  |   ||||  | |  | ||||||| || ||||  |||||| | ||||| ||| | || ||||| |||||  | ||||||||||||||||| ||||||||||| ||||||
gtaatttctctttacttgtttgatagttaagtaaaacttttggttctagtttttagtctagcttactcttggtgctttgattttcactgctttgcgatgaaacaatggtgttgcaatctcatactgaaatgattgttgatgtgattgacagAATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAG

upper sequence: GRMZM2G029685_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G04920.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------------------------------------------------------gactgtcttgagccttcagatga-cgccattcactgtttgctgttagcctctgtttgatacacctgtccgtaggtgctaatgttctgtttttc--gtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG
                                                                                              ||   |  | |||  |  ||| |    |   |  | | |  | ||   ||  || |  |   | | |   ||  |    ||| | ||| | |   || | ||||| || ||||  || ||| | ||||||||| | || || || |||||| | ||||||||||||||||||||||||||||| ||||||
gtaaatgctttttccactcttgtttccattgttatatattgctactcacattgacccgtcttaaatcattactcttgctcattactgtttgtctgaaaattataagctatgtgataagtttcggactttatatcgtattgcacttggtgttctctgcatctttatacttaaacatgctttgtctatgtggttggcagAATGGACTTGACACTAAGATTGAGAAGTCAAGGAAACAAATTAAGGAAAGGAAGAACAGGGCGAAGAAAATCCGTGGTGTTAAGAAG

upper sequence: GRMZM2G029685_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0151g00900.t01 (Vitis vinifera), 3'ss of exon 3
gactgtcttgagccttcagatgacgccattcactgtttgctgttagcct-ctgtttgatacacctgtccgtaggtgctaatgttctgtttttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG
 ||     ||  |  | ||   ||         | | |    |||   | || || || |||    ||  |   |   |   |      ||   |   ||||| ||  | | ||||||||| || |||||| | ||||| ||||||||| | ||||||||||| |||||  |||| || |||||||||
-acaacaatgtacacttagtgaacaaggaatcttatcttgctttattttgctattcgaaacatgcttctctttctctgaccatagcaacttgtctgcgcagAATGGATTGGATACCAAGGTGGAAAAGTCAAGGAAGCAAATGAAGGAAAGGAAGAACAGGGCCAAGAAGGTCCGAGGAGTGAAGAAG

upper sequence: GRMZM2G029685_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------------gactgtcttgagccttcagatgacgccattcactgtttgctgtta-gcctctgtttgatacacctgtccgtaggtgctaatgttctgtttttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG
                                                             | || |   ||  | |||    |||  ||| ||| | |   |  |   ||||  |      |  |||  ||   ||  | |  |  |  |   ||||| || || ||||||||||| ||||||||  | |||||||| ||||| || |||||| |  ||||||| ||| | ||||||||||||
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|211014258|gb|FL283800.1|FL283800
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
EST: gi|15079941|gb|BI388886.1|BI388886
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
EST: gi|211008706|gb|FL283775.1|FL283775
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAA
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAA
EST: gi|211011487|gb|FL283793.1|FL283793
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
EST: gi|211014263|gb|FL283805.1|FL283805
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
EST: gi|211014266|gb|FL283808.1|FL283808
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
EST: gi|60397441|gb|DN230257.1|DN230257
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
EST: gi|60355885|gb|DN222858.1|DN222858
EST:     ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGG                         AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT
genomic: ACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

CCGAACCAACTTCGGAGGCGGCAAGTCCACCGGCTTCGGTCTCATCTACGACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

CCGAACCAACTTCGGAGGCGGCAAGTCCACCGGCTTCGGTCTCATCTACGACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 91

CCGAACCAACTTCGGAGGCGGCAAGTCCACCGGCTTCGGTCTCATCTACGACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

CCGAACCAACTTCGGAGGCGGCAAGTCCACCGGCTTCGGTCTCATCTACGACAACCTTGAGGCCGCCAAGAAGTTCGAGCCCAAGTACCGCCTCATCAGGgtatatcatt ... tcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctctgtttgatacacctgtccgtaggtgctaatgttctgtttttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG
                            tgctaat  putative branch site (score: 85)
                                    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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gactgtcttgagccttcagatgacgccattcactgtttgctgttagcctctgtttgatacacctgtccgtaggtgctaatgttctgtttttcgtcgacagAACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG