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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttcttcattgcttctaacattacatttcaatagcacttgatggctttggcaacacaggctgctaattagtgtactgttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG

Basic information

species Zea mays
transcript GRMZM2G091151_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g24250.1 (Oryza sativa), 3'ss of exon 2
gtgcttcttcattgcttctaacattacatttcaatagcacttgatggctttggcaacacaggctgctaattagtgtactgttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
|||||| |  || |   |  |  ||| | |  | ||     ||| |      || |  |||  |  | ||| |||| ||    ||||||||| || |  ||||||||||  |||||||| |  || ||||||||||||||||| ||||||||||||||||||||||||||||||
gtgcttttctatcgtcgcccatgtta-actctagtaa----tga-gctcagagctatgcagttttttgattggtgtgct---ttggcagGTTTACAACAGAGCAGGTTCGTAATCTTGATAGGAACAAGCAGTGGTCTAGAGCTCTTGATGGCTCCAATTATCTACCTGGAATG

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G22190.1 (Glycine max), 3'ss of exon 3
-----gtgcttcttcattgcttctaacattac-atttcaatagcacttgatggctttggcaacacaggct--gctaattagtgtactgttctg---gcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
      || |   |   ||||  |   |     | |||  || |  || |     |     |||    ||  | | |||  |||  |  |||    |||| ||| ||    |  | |||  | | |||||||||||||||||||||||||| || |||||||| || | ||| || |||||||||
attctctgttctctttatgctgttgttaccttgaattctttaactgttaaactactaatatacatgatctaagttcattcatgtggttctctatctgcagATTCGCTGCAAAAGAAGTTGAACAACTTGACAAAAATAAGCAGTGGTCTAGGGCTCTTGATGGTTCTAGTTACCTTCCTGGAATG

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G08500.2 (Glycine max), 3'ss of exon 3
-------gtgcttcttcattgcttctaacattacatttcaatagcacttgatggct--ttggcaacac--aggctgctaattagtgtactgttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
       || ||  ||   |  || | || ||  |||     |    || |   ||  |  |||  |   | | |  |   ||  ||  | |    |||| ||||||    |  | |||  | | |||||||||||||||||||||||||| || |||||||| || | ||| || || ||||||
attctctgttctctttatgttgttgttaccttgaattctttaaatgattaactactaatatgcattatctaagttcattcatatggttatctatctgcagATTCACTGCAAAAGAAGTTGAACAACTTGACAAAAATAAGCAGTGGTCTAGGGCTCTTGATGGTTCTAGTTACCTTCCCGGAATG

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G22350.2 (Arabidopsis thaliana), 3'ss of exon 2
-----gtgcttcttcat----tgcttctaacattacatttcaatagcacttgatggctttggcaacacaggctgctaattagtgtactgttc--tggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
       ||||   |||      |||||  |||    | |||||    |||      ||  |   |   |  ||     |   || || | |  |  |||||| | ||  |  || ||     | |||||||| |||| |||||||||||| || |||||||||||| | ||||| || ||||||
catgatagcttgaacatattactcttctttcatgttttgtcaatttttctttgatttttcagttcctttgtatgaaggcttcggtgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G22410.1 (Arabidopsis thaliana), 3'ss of exon 1
-----gtgcttcttcat----tgcttctaacattacatttcaatagcacttgatggctttggcaacacaggctgctaattagtgtactgttc--tggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
      |  || |||||      |||||  |||    | |||||    |||      ||  |   |      ||     |   || || | |  |  |||||| | ||  |  || ||     | |||||||| |||| |||||||||||| || |||||||||||| | ||||| || ||||||
tatttatattttttcatattactcttctttcatgttttctcaatttttctttgatttttcagttcctttttatgaaggcttcggtgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G22285.1 (Arabidopsis thaliana), 3'ss of exon 3
-----gtgcttcttcat-tgcttctaacattacatttcaatagcacttgatggctttggcaacacaggctgctaa-----ttagtgtactgttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
       ||||   ||| |   |||    | |  | |    |    ||  | | |||  ||   |    |  | |     |  ||||  |    |  |||||| | ||  |  || ||     | |||||||| |||| |||||||||||| || |||||||||||| | ||||| || ||||||
cttgatagcttgaacatattactcttctttcatgtcttgtcaaattttctttgattttacagttcctttttatgaaggcttcggtgttatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG

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|211066153|gb|FL067272.1|FL067272
EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
EST: gi|211066159|gb|FL067278.1|FL067278
EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
EST: gi|211068890|gb|FL067279.1|FL067279
EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTC-CTAAAGGAGCAGGTTCTAAATCTTGACAAAAAATAAGCA
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAA-GGAGCAGGTTCTAAATCTTGACAAAAA-TAAGCA
EST: gi|211068893|gb|FL067282.1|FL067282
EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTC-CTAAAGGAGCAGGTTCTAAATCTTGACAAAAAATAAGCA
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAA-GGAGCAGGTTCTAAATCTTGACAAAAA-TAAGCA
EST: gi|211066145|gb|FL067264.1|FL067264
EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
EST: gi|211066152|gb|FL067271.1|FL067271
EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
EST: gi|211066151|gb|FL067270.1|FL067270
EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
EST: gi|211066150|gb|FL067269.1|FL067269
EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
EST: gi|211066157|gb|FL067276.1|FL067276
EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GGTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGNGGTCTAN
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
EST: gi|211066156|gb|FL067275.1|FL067275
EST:     GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAG                         GTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG
genomic: GAGATTAATGATCCATCGTTAGAAGATATTCGACATGTTCTGAATCCAAGgtgcttcttc ... gttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcacttgatggctttggcaacacaggctgctaattagtgtactgttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
                             tgctaat  putative branch site (score: 2)
                                           ctgttct  putative PPT
                                taattagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttcttcattgcttctaacattacatttcaatagcacttgatggctttggcaacacaggctgctaattagtgtactgttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA