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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgaactcgcatccgatttccccaatactttcttcgattctttcctgttcctcaccttggttcgatctgccacgccggtgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG

Basic information

species Zea mays
transcript GRMZM2G052713_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052713_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 1
gtaacgaactcgcatccgatttccccaatactttct-tcgattctttcctgttcctcaccttggttcgatctgccacgccggtgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG
|||| || | ||||| |    ||  |  | |   |  ||    |  ||     ||  ||||  ||||   | |  | |  | |||||||||||||||||||||||||||| ||||||||||| || ||||||||||||||||| ||| | ||||||||||| |||||||||||||| |||||||||
gtaaagatcccgcattcagcctcttctgttccccccctctccgcgatctgaaaccgtacct--gttcttcccggaatgg-gctgcagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAG

upper sequence: GRMZM2G052713_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G37730.1 (Glycine max), 3'ss of exon 1
---------------------gtaacgaactcgcatc-cgatttccccaatactttcttcgattc----------tttcctgttcctcaccttggttcgatctgccacgccggtgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG-
                      |  |    ||||  |   ||| |   |||| | |||||| | |          ||| |  |||   |  | | ||   |||    |||    ||||||||| ||||| ||| |||||||| ||||||| || || || || ||||| ||||| ||  |||||||||||||||||||||||||||| || |||||| 
gttccttcgttcatcattctattccctctttcgctccataattacaataataatctcttcgttccaatatttcttttttccattctaaaattcgttttcctcttttccgcattcgcagATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGACTCCGAGAAGCACAAGGTCGAATACGAGG

upper sequence: GRMZM2G052713_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA14G40430.2 (Glycine max), 3'ss of exon 1
gtaacgaactcgca-tccgatttccccaatactttcttcgattctttcctgttcctcaccttggttcgatctgccacgccggt-gcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG
         ||  | | | ||| || |  |  || | |   || |||| | ||       ||| ||    ||    |  |  | ||||||||| ||||| ||| |||||||| ||||||| || || || || ||||| ||||| ||  |||||||||| ||||||||||||||||| || ||||||
---gttcgttcataattctattccctctttcgttccattttttttttcatttttgaatgattgttttcccctttttccgcattcgcagATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAG

upper sequence: GRMZM2G052713_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 2
gtaacgaactcgcatccgatttccccaatactttcttcgattctttcctgttcctcaccttggttcgatctgccacgccggtgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG
||| |   ||||  |  |||    | |||  |   | |||     |   ||| || ||    ||||  |   |   |     ||||||||| |||||  | || |||||| ||||||| || || || || ||||||||||||||  |||| || || ||||||||||||||||| || ||||||
gta-ctctctcgattatgatgattc-aatcttgattgcgaggagattgagttgctgactc--gttcattaatctttgatttggcagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAG

upper sequence: GRMZM2G052713_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ11600 (Selaginella moellendorffii), 3'ss of exon 1
gtaacgaactcgcatccgatttccccaatactttcttcgattctttcctgt-tcctcaccttggt-tcgatctgccacgccgg---tgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG
                                |   | |||| |  | ||  |||   |   |   |||||| |||  |  ||    ||||||  | ||||||||  |||| || || |||||||| || || || ||||||||||||||| | ||||| |||||||||||||| ||| |  |||| |||
-------------------------------gtgagtggattttcgcttggatccgtgctgagacatcgatc-gccgtgttggatgcgcagATTAGATTCATCCTCTTGCAAAATCGCCAGGGGAAGACTCGTCTCGCCAAGTACTATGTCCCGCTCGAAGACTCCGAGAAGCAAAAGCTCCAGTATGAG

upper sequence: GRMZM2G052713_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ09792 (Selaginella moellendorffii), 3'ss of exon 1
gtaacgaactcgcatccgatttccccaatactttcttcgattctttcctgt-tcctcaccttggt-tcgatctgccacgccgg---tgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG
                                |   | |||| |  | ||  |||   ||  |   |||||| |||  |  ||    ||||||  | ||||||||  |||| || || |||||||| || || || ||||||||||||||| | ||||| |||||||||||||| ||| |  |||| |||
-------------------------------gtgagtggattttcgcttggatccgtgccgagacatcgatc-gccgtgttggatgcgcagATTAGATTCATCCTCTTGCAAAATCGCCAGGGGAAGACTCGTCTCGCCAAGTACTATGTCCCGCTCGAAGACTCCGAGAAGCAAAAGCTCCAGTATGAG

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|211344147|gb|FL188317.1|FL188317
EST:     GTCCTTCCCAATTCTCAGGCAACCCCGTCGTCTTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAG
genomic: GTCCTTCCCAATTCTCAGGCAACCCCGTCGTCTTCCGCCATGgtaacgaact ... gccggtgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAG
EST: gi|211344138|gb|FL188308.1|FL188308
EST:     ACGACTCTGTCCTTCCCAATTCTCAGGCAACCCCGTCGTCTTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAG
genomic: ACGACTCTGTCCTTCCCAATTCTCAGGCAACCCCGTCGTCTTCCGCCATGgtaacgaact ... gccggtgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAG
EST: gi|211341751|gb|FL188301.1|FL188301
EST:     ACGACTCTGTCCTTCCCAATTCTCAGGCAACCCCGTCGTCTTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAG
genomic: ACGACTCTGTCCTTCCCAATTCTCAGGCAACCCCGTCGTCTTCCGCCATGgtaacgaact ... gccggtgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAG
EST: gi|211341749|gb|FL188299.1|FL188299
EST:     GTCCTTCCCAATTCTCAGGCAACCCCGTCGTCTTCCGCCATG                         ATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAG
genomic: GTCCTTCCCAATTCTCAGGCAACCCCGTCGTCTTCCGCCATGgtaacgaact ... gccggtgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttcgattctttcctgttcctcaccttggttcgatctgccacgccggtgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG
                    tcctcac  putative branch site (score: 2)
        attcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgaactcgcatccgatttccccaatactttcttcgattctttcctgttcctcaccttggttcgatctgccacgccggtgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC