Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttattttattaatatactcataaaaatggaataaatcattgaaattttctgtcatttgttttccaatatgtgttatctctttctattaacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG

Basic information

species Zea mays
transcript GRMZM2G074169_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074169_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g37420.2 (Oryza sativa), 3'ss of exon 2
tgtttattttat-taatatac-tcataaaaatggaataaatcattgaaattttctgtcatttgttttccaatatgtgttatctc-tttctattaacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG
  || || | || |    ||  |           || ||||  |   ||| |   |  |||| |   |       |   ||||| |   | |||||||||||||| |||||||| ||| |||||||||||||||| |||||||| ||||| || |||||||| |||||||
-tttaatgtcatctgccgtatgttgcttgccgataagaaattgtgctaatatggag--atttatgcacttgaccataacatctcatccttgttaacatttcagGTATATGATGTTACTTCTTTTATGGATGAGCACCCTGGTGGCGATGAAGTGTTGCTAGCAGTAACTG

upper sequence: GRMZM2G074169_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G13840.2 (Glycine max), 3'ss of exon 2
tgtttattttattaatatactcataaaaatggaataaatcattgaaattttctgtcatttgttttc--caatatgtgttatctctttctattaacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG
    ||  | | |  |  | |   |    | |  | | |  | |   | || || | || ||||    || |        |    | ||   |  || | |||||||||||||||| ||||| ||||| || ||||| || || |||||||||||| || ||| ||| |
-aactacataacttttgaattt-cagttctagcttgagttctagttttgttatgacgttagtttctgtcactgaacaaagttgtgtgcttcaacaatattagGTGTATGATGTCACCCCTTTCATGGAGGATCATCCCGGAGGTGATGAGGTTTTGTTATCTGCAACAG

upper sequence: GRMZM2G074169_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G41010.3 (Glycine max), 3'ss of exon 2
tgtttattttattaatatactcataaaaatggaataaatcattgaaattttctgtcatttgttttccaatatgtgttatctctttctattaacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG
                                  ||     || |   ||||||||| |        || |   ||||| |  ||| ||    || | |||||||||||||||| ||||| ||||| || ||||| || || |||||||||||| || ||| ||| |
----------------------------------tatgatgttaa---tttctgtcactg-------aacaaa-gttatgtgcttcaatg---atattaggtgtatgatgtcacccctttcatggaggatcatcccggaggtgatgagGTTTTGTTATCTGCAACAG

upper sequence: GRMZM2G074169_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G41010.2 (Glycine max), 3'ss of exon 2
---tgtttattttattaatatactcataaaaatggaataaatcattgaaatttt-ctgtcatttgttttccaatatgtgttatctctttctattaacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG
   |   ||  || | ||| |       |    |   |  |   |||  ||  |  |    | |||     || |   ||||| |  ||| ||    || | |||||||||||||||| ||||| ||||| || ||||| || || |||||||||||| || ||| ||| |
aactacgtaacttttgaatttcagttctagctcgagttctagttttgttatgatgttaatttctgtcactgaaca-aagttatgtgcttcaatg---atattagGTGTATGATGTCACCCCTTTCATGGAGGATCATCCCGGAGGTGATGAGGTTTTGTTATCTGCAACAG

upper sequence: GRMZM2G074169_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G53560.1 (Arabidopsis thaliana), 3'ss of exon 2
-------tgtttattttattaatatactcataaaaatggaataaatcattgaaattttctgtcatttgttttccaatatgtgttatctctttctattaacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG
        ||  ||||  || || |     | ||     | || |  |    | |||      | |  ||    |  || ||| ||    ||   ||     || ||||||||||||| ||||| || |||||||| |||||||| || ||||| || ||| |  |   ||| |
agcccctcgtagatttagttgat-tctatgttaattcacactagagaaacagagtttgtgtctactacttggttatgatctgtgattg--ttgcgtt----ctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTCTTGTTGTCCTCAACAG

upper sequence: GRMZM2G074169_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv16s0098g01230.t01 (Vitis vinifera), 3'ss of exon 2
--tgtttattttatta--atatactcataaaaatggaataaatcattgaaattttctgtcatttgttttccaatatgtgttatctctttctattaacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG
  ||    ||| | |   | ||| |  |  |  | |   |  | |||  | || | | | |||||||    ||  | |   |||||  ||||||    |  |||||||||||||| ||||| || |||||||| |||||||| || ||||| ||||||||| | | |||||
cctgcaattttgaatgtgacatagttttggatgttggtgactttattcta-ttctatttaatttgttgataaaattttaaaatctccatctatt---gtaacagGTGTATGATGTAACTCCGTTCATGGATGATCATCCTGGAGGTGATGAAGTTTTGCTATCAGCAACTG

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|211368307|gb|FL144000.1|FL144000
EST:     TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAG                         GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
genomic: TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAGgtgctgtttt ... aacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
EST: gi|211368308|gb|FL144001.1|FL144001
EST:     TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAG                         GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
genomic: TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAGgtgctgtttt ... aacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
EST: gi|32937079|gb|CF041898.1|CF041898
EST:     GATCATCATCGCCGGCAAG                         GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
genomic: GATCATCATCGCCGGCAAGgtgctgtttt ... aacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
EST: gi|116825751|gb|EC869489.1|EC869489
EST:     TCGCCAAGCACAACGTCAACAAGGACTGCTGGATCATCATCGCCGGCAAG                         GTGTATGATGTCACTCCTTTTATGGATGAGCATCC
genomic: TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAGgtgctgtttt ... aacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCC
EST: gi|211103108|gb|FL195442.1|FL195442
EST:     TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAG                         GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
genomic: TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAGgtgctgtttt ... aacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
EST: gi|211368309|gb|FL144002.1|FL144002
EST:     TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAG                         GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
genomic: TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAGgtgctgtttt ... aacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
EST: gi|211368306|gb|FL143999.1|FL143999
EST:     TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAG                         GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
genomic: TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAGgtgctgtttt ... aacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
EST: gi|211368305|gb|FL143998.1|FL143998
EST:     TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAG                         GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
genomic: TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAGgtgctgtttt ... aacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
EST: gi|211368303|gb|FL143996.1|FL143996
EST:     TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAG                         GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
genomic: TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAGgtgctgtttt ... aacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
EST: gi|211103116|gb|FL195450.1|FL195450
EST:     TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAG                         GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
genomic: TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAGgtgctgtttt ... aacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
EST: gi|211105581|gb|FL195453.1|FL195453
EST:     TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAG                         GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
genomic: TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAGgtgctgtttt ... aacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
EST: gi|211368304|gb|FL143997.1|FL143997
EST:     TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAG                         GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
genomic: TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAGgtgctgtttt ... aacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
EST: gi|211467880|gb|FL454208.1|FL454208
EST:     TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAG                         GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
genomic: TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAGgtgctgtttt ... aacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
EST: gi|211368302|gb|FL143995.1|FL143995
EST:     TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAG                         GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
genomic: TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAGgtgctgtttt ... aacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
EST: gi|76284386|gb|DV023954.1|DV023954
EST:     TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAG                         GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT
genomic: TCGCCAAGCACAACGTCACCAAGGACTGCTGGATCATCATCGCCGGCAAGgtgctgtttt ... aacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttctgtcatttgttttccaatatgtgttatctctttctattaacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG
                                         tattaac  putative branch site (score: 1)
                                     tttctattaacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttattttattaatatactcataaaaatggaataaatcattgaaattttctgtcatttgttttccaatatgtgttatctctttctattaacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG