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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTGGTTGGATGATGGGACAAAGGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttcttaaggtggatattaataaaaacttttataaaatgtgtctgttgttgcctgttggtaaggtttattgatgccatcatatggactgtgaaaat...

Basic information

species Zea mays
transcript GRMZM2G040017_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040017_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g55940.2 (Oryza sativa), 5'ss of exon 9
TATTGGTTGGATGATGGGACAAAGGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttcttaaggtggatattaataaaaacttttataaaatgtgtctgtt--gttgcctgttggtaaggtttattgatgccatcatatggactgtgaaaat
 ||||||||||||||||| |||| ||||||||||||||| || ||||| || |||||||| |||||||||||||| || || || |||||||||||||||||||||| ||  |    ||||||| ||  | ||| ||||    || ||| |   |     ||| || | | |  |   ||   |  ||||   || | | ||
CATTGGTTGGATGATGGGGCAAAAGATGGACTTGAATTTCCAACTATTCGAAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttattgtgtgaaatattaagaattattttgataagggatgcctgcttaatgaagagtttgtcaagct-gtgtttgtttttgtatgccttg-gcacat

upper sequence: GRMZM2G040017_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv09s0018g01840.t01 (Vitis vinifera), 5'ss of exon 10
TATTGGTTGGATGATGGGACAAAGGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttcttaaggtggatattaataaaaacttttataaaatgtgtctgttg-ttgcctgt-tggtaaggtttattgatgccatcatatggactgtgaaaat---
| |||||||||| |||||||||   ||||||||||||||||| || |||||||| || |||||||| ||  | ||||| || || ||||||||| | |||||  ||| | ||| |    |||        ||||||      || |  ||   |  ||  | |||  |  | | ||| |    |  | | |    ||   ||   
TGTTGGTTGGATTATGGGACAACCAATGGACTTGAATTTTCAACTCTTTGAGACTGCCACTCTCTTTATCGCGGTGCTAGTAGTGGCATTTATGTTGCAGgtttgttatcaagttcctcatttcc-----cttttagttttggttttggtcaatcaccgatatggacacatatcttgttaattttgtctaggtcttgtgcatcat

upper sequence: GRMZM2G040017_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S79_95V6.1 (Physcomitrella patens), 5'ss of exon 10
TATTGGTTGGATGATGGGACAAAGGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttcttaa------ggtggatattaataaaaact--tttataaa----atgtgtctgttgttgcctgt-tggtaaggtttattgatgccatcatatggactgtgaaaat--------------
 ||||| |||   |||||       |||||| |||||||| | || |||||||| |||||||| ||||||||||| || ||||| || || ||||| || ||  |   | ||       ||   | |   |   |||    | |||||    || |   |    || | ||| || | |    |  |  | |  || | |    |   | ||               
CATTGGATGGCCCATGGGGACCCACATGGACCTGAATTTTGAACTGTTTGAGACGGCAACTCTATTCATAACAGTTCTGGTGGTTGCCTTGATGCTTCAAgtgagaaatcaatcatccagtctctgtctctgttaaccaactaataaatccgatattcttaggtttccttgtgtgctcactcgtgattgttctgtc-tctaattttccataactccgaatgtaccag

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|211272295|gb|FL440029.1|FL440029
EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGCACCGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|149085153|gb|EE174657.2|EE174657
EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATTTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|211010290|gb|FL457993.1|FL457993
EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|91868897|gb|EB400200.1|EB400200
EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|32837305|gb|CD976983.1|CD976983
EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGAT
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGAT
EST: gi|32836604|gb|CD976282.1|CD976282
EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|148972711|gb|EE023671.2|EE023671
EST:     AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAG                         GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttctt ... ttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTGGTTGGATGATGGGACAAAGGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTGCTTGTGGTAGCATTTATGCTACAGgtaggttcttaaggtggatattaataaaaacttttataaaatgtgtctgttgttgcctgttggtaaggtttattgatgccatcatatggactgtgaaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaaa