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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaacaatttcttagtttctgcatcatgtaacttttactgggataatgattagactaattttgtattgcctctactgctctacagGAATTCAGCACTAAGAACAAGCTGCTTATCACGGGAACACCTTTGCAGAACAGTGTGGAAGAGCTTTG

Basic information

species Zea mays
transcript GRMZM2G141258_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os07g46590.1 (Oryza sativa), 3'ss of exon 2
gtatgaa-acaatttcttagtttctgcatcatgtaacttttactggg-ataatgattagactaattttgtattgcctctactgctctacagGAATTCAGCACTAAGAACAAGCTGCTTATCACGGGAACACCTTTGCAGAACAGTGTGGAAGAGCTTTG
||||||| |  ||||| |    |    || |       || |||      || ||| |  |||||||   | |||| | ||      ||||||||||||||||||||| ||||| || ||||| || || || ||||| ||||| || |||||||| ||
gtatgaacagtatttcctgaactaaaaataagagtgagttgactacctggaaagatgactctaatttc--actgcccccac------acagGAATTCAGCACTAAGAATAAGCTTCTCATCACCGGGACCCCATTGCAAAACAGCGTTGAAGAGCTCTG

upper sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 13
gtatgaaacaatt-tcttagtttctgcatcatgtaacttttactgggataatgattagactaattttgtat-tgcctctactgctctac-agGAATTCAGCACTAAGAACAAGCTGCTTATCACGGGAACACCTTTGCAGAACAGTGTGGAAGAGCTTTG
||||| |||| || ||||| ||| |   || ||| | | ||  |  ||||  | |||   |  | | || | |   | | ||  |||   ||||||| ||||| ||||||||| |||||||||| || || ||| | ||||||||||||||||| || ||
gtatgtaacatttgtcttaatttatttctc-tgtgattgtt--tatgatagagtttaatattttatggtttgtttttgtgctaatcttttagGAATTTAGCACCAAGAACAAGTTGCTTATCACCGGTACTCCTCTACAGAACAGTGTGGAAGAACTATG

upper sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 13
gtatgaaacaatt-tcttagtttctgcatcatgtaacttttactgggataatgattagacta-attttgtattgcctctactgctctacagGAATTCAGCACTAAGAACAAGCTGCTTATCACGGGAACACCTTTGCAGAACAGTGTGGAAGAGCTTTG
||||| |||| || ||||| ||| |   |  || || | ||  ||  | | |   |    ||   ||||| ||    ||| |  | |  ||||||| ||||| ||||||||  |||||||||| || || ||| | ||||||||||||||||| || ||
gtatgtaacatttctcttaatttattt-ttgtgcaattgtttatgatagagtttattttttatggtttgtttttttgctaatctttt--agGAATTTAGCACCAAGAACAAATTGCTTATCACTGGCACTCCTCTACAGAACAGTGTGGAAGAACTATG

upper sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 13
-----------------------------------------------------------------------------------gtatgaaacaatttcttagtttctg------catcatgtaacttttactgg-gataatga------ttagactaattttgtattgc-ctctactgctctacagGAATTCAGCACTAAGAACAAGCTGCTTATCACGGGAACACCTTTGCAGAACAGTGTGGAAGAGCTTTG
                                                                                    |     | |||||  | | || ||      ||  |  |||  |||| |   | | ||||      || |  ||||  |  ||    |  | ||  ||| |||||||||||  | ||||||||| |||| ||||| || || || || ||||||||||| |||||||||||
gtatgctgtatttcttaatgatatgtttacgttggccttttatttatgaagcacaatagtaaacaatcctctgggtacacatatttcattataattttctggcttttgtcttttcaataaataatatttatttttgttgatgagtcttatttggttaatgctagatgatgccttgcttttctgcagGAATTCAGTGCCAAGAACAAGTTGCTGATCACTGGTACTCCATTACAGAACAGTGTTGAAGAGCTTTG

upper sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 13
lower sequence: PP1S317_10V6.1 (Physcomitrella patens), 3'ss of exon 14
-----------gtatgaaacaatttcttagtttctgca-tcatgtaacttttactgggataatgattagactaattttgtattgcctctactgctctacagGAATTCAGCACTAAGAACAAGCTGCTTATCACGGGAACACCTTTGCAGAACAGTGTGGAAGAGCTTTG
             |  |    |||    |  || || | |  ||  | |   | ||  |   ||  |   | | |||   ||   | ||  | | | ||||||||||||||| || |||||| ||||  | || ||||| || |||||||||||||| ||||| |||||
tatttatatttccaaaaggatattaaccatattttgtagttttgacattgcaaatgctaagttgccttatccattttaaaatcatcact-ttacccaacagGAATTCAGCACCAAAAACAAGGTGCTGGTTACAGGAACTCCGTTGCAGAACAGTGTTGAAGAACTTTG

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|33095165|gb|CF055159.1|CF055159
EST:     CCCACCGGTTGAAAAATTGTGAAAGCGTCACTGTTATACAACCCCTTTTG                         GAATTCAGCACTAAGAACAAGCTGCTTATCACGGGAACACCTTTGCAGAA
genomic: CCCACCGGTTGAAAAATTGTG-AAGCGTCACTG-TATACAA-CCCTTTTGgtatgaaaca ... tgctctacagGAATTCAGCACTAAGAACAAGCTGCTTATCACGGGAACACCTTTGCAGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttactgggataatgattagactaattttgtattgcctctactgctctacagGAATTCAGCACTAAGAACAAGCTGCTTATCACGGGAACACCTTTGCAGAACAGTGTGGAAGAGCTTTG
                      gactaat  putative branch site (score: 2)
                                      cctctact  putative PPT
                  attagactaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaacaatttcttagtttctgcatcatgtaacttttactgggataatgattagactaattttgtattgcctctactgctctacagGAATTCAGCACTAAGAACAAGCTGCTTATCACGGGAACACCTTTGCAGAACAGTGTGGAAGAGCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT