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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctaaacaattcctatgaattttctgcgttccaaaggggcccctcagtctctatgcatttgtccatcaaaggttgcaaacttatttctcgtttacccaagGTGGTATGCCAAACGATTTCTACATCCTGACATTGTTGCCCGCTACGACTACATATTTATCTGGGATGAAGATCTTGGTGTCGAACATTTTAATGCAGAG

Basic information

species Zea mays
transcript GRMZM5G801369_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G801369_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 6
cctaaacaattcctatgaatttt-ctgcgttccaa-aggggcccctcagtctctatgcatttgtccatcaaaggttgcaaactta---tttctcgtttacccaagGTGGTATGCCAAACGATTTCTACATCCTGACATTGTTGCCCGCTACGACTACATATTTATCTGGGATGAAGATCTTGGTGTCGAACATTTTAATGCAGAG
  ||||  |||   |   ||  |  || |||     |    |   |    | ||||| ||||| | | |||||| |      ||     || |  ||||  ||||||||||||||||  ||||| |||||||||| ||||||||||  || ||||||||||||||||||||||| |||||  ||||  ||||||| |||||||||
-gtaaattattgtaacagatcctgttgtgttttttcatcttctagtttagcactatgtatttgacaaccaaaggctaagtgttttactctttttttttatacaagGTGGTATGCCAAGAGATTTTTACATCCTGATATTGTTGCCCCGTATGACTACATATTTATCTGGGATGAGGATCTAAGTGTACAACATTTCAATGCAGAG

upper sequence: GRMZM5G801369_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 7
cctaaacaattcctatgaattttctgcgttccaaaggggcccctcagtctctatgcatttgtccatcaaaggttg--caaacttatttctcgtttacccaagGTGGTATGCCAAACGATTTCTACATCCTGACATTGTTGCCCGCTACGACTACATATTTATCTGGGATGAAGATCTTGGTGTCGAACATTTTAATGCAGAG
               | | |  |||| ||     |  ||    | ||| |       |||||| |  |    ||   | || || | |   | ||     |||||||| || ||  | ||| | ||||||||  ||||  |    || || ||||||||||| ||||||||||||||||| || || ||||| ||||| || 
--------------gttagtcatctg-gtcatttaccggttattaagtat------gtttgtcgagtatgtttttatcgaaattctctactggttttggcagGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT

upper sequence: GRMZM5G801369_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
cctaaacaattccta-tg-aattttctgcgttccaaaggggcccctc-agtctctatgca--tttgtccatcaaaggttgcaaacttattt-ctcgtttacccaagGTGGTATGCCAAACGATTTCTACATCCTGACATTGTTGCCCGCTACGACTACATATTTATCTGGGATGAAGATCTTGGTGTCGAACATTTTAATGCAGAG
  |||  |||    | || |  |     || |  |        | || | |    ||| |  ||| || | ||||     ||   | |  |  |  | |     ||||||||||| ||  ||||| | ||||||||  ||||  |    || || || |||||||| ||||||||||||||||| ||||| || || |||||||| 
-gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtcatgaaaatttatcta-caaaatcctcaccttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT

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|6021059|gb|AW065987.1|AW065987
EST:     AAAAGGGCTG-CCATGTGAGTG-CACAAAGCAGACCAAATG                         GTGGTATGCCAAACGATTTCTACATCCTGACATTGTTGCCCGCTACGACTA
genomic: AAAAGGGCCGTCCATGTGAGTGTCACAAAGCAAACCAAATGgtgagttgtt ... tttacccaagGTGGTATGCCAAACGATTTCTACATCCTGACATTGTTGCCCGCTACGACTA
EST: gi|71438212|gb|DR819262.1|DR819262
EST:     GAGTGGTCAAAAAGGGCCGTCCATGTGAGTGTCACAAAGCAAACCAAATG                         GTGGTATGCCAAACGATTTCTACATCCTGACATTGTTGCCCGCTACGACTA
genomic: GAGTGGTCAAAAAGGGCCGTCCATGTGAGTGTCACAAAGCAAACCAAATGgtgagttgtt ... tttacccaagGTGGTATGCCAAACGATTTCTACATCCTGACATTGTTGCCCGCTACGACTA
EST: gi|149062889|gb|EE157609.2|EE157609
EST:     GAGTGGTCAAAAAGGGCCGTCCATGTGAGTGTCACAAAGCAAACCAAATG                         GTGGTATGCCAAACGATTTCTACATCCTGACATTTGT-GCCCGCTACGACT
genomic: GAGTGGTCAAAAAGGGCCGTCCATGTGAGTGTCACAAAGCAAACCAAATGgtgagttgtt ... tttacccaagGTGGTATGCCAAACGATTTCTACATCCTGACATT-GTTGCCCGCTACGACT
EST: gi|71301944|gb|DR787048.1|DR787048
EST:     GAGTGGTCAAAAAGGGGCGTCCATGTGAGTGTCACAAAGCAAACCAAATG                         GTGGTATGCCAAAC
genomic: GAGTGGTCAAAAAGGGCCGTCCATGTGAGTGTCACAAAGCAAACCAAATGgtgagttgtt ... tttacccaagGTGGTATGCCAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtctctatgcatttgtccatcaaaggttgcaaacttatttctcgtttacccaagGTGGTATGCCAAACGATTTCTACATCCTGACATTGTTGCCCGCTACGACTACATATTTATCTGGGATGAAGATCTTGGTGTCGAACATTTTAATGCAGAG
                                  cttatttctcgttt  CT-rich tract
                               aaacttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctaaacaattcctatgaattttctgcgttccaaaggggcccctcagtctctatgcatttgtccatcaaaggttgcaaacttatttctcgtttacccaagGTGGTATGCCAAACGATTTCTACATCCTGACATTGTTGCCCGCTACGACTACATATTTATCTGGGATGAAGATCTTGGTGTCGAACATTTTAATGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- -aaacaat
- - - - - - - - - -ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - atgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgcaa