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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattcatctaatagtttctttacttcattagccaactatgttcttatctattatcaatttttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG

Basic information

species Zea mays
transcript GRMZM2G065105_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065105_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g50120.2 (Oryza sativa), 3'ss of exon 8
--------gtaa--attcatctaatagtttcttt---------act--tcattagccaactatgttcttatctattatcaatttttttaaat--agGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG
        ||||  |  |    ||   | ||| |         ||   | ||  | ||||    || || | ||||   | | || ||||||  |||||||||||||||| |||||||||||| ||||||||||||||||||||||||||||||| |||||| | ||||||
gtaggcaggtaagtaccctctcaacgatatctattaaaaaggcaccgataatctgtcaaccccattattgtttattcatactgttcttaaatgtagGTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGAGTCATAGCAATAATAGTCGTTAAG

upper sequence: GRMZM2G065105_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g50120.1 (Oryza sativa), 3'ss of exon 8
gtaaat--tcatctaatagtttcttt---------act--tcattagccaactatgttcttatctattatcaatttttttaaat--agGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG
|||| |   |    ||   | ||| |         ||   | ||  | ||||    || || | ||||   | | || ||||||  |||||||||||||||| |||||||||||| ||||||||||||||||||||||||||||||| |||||| | ||||||
gtaagtaccctctcaacgatatctattaaaaaggcaccgataatctgtcaaccccattattgtttattcatactgttcttaaatgtagGTTGCAACTGATCGCTGCATCATGGCCTTGCTTTTTCTCATTGTTGCTGGAGTCATAGCAATAATAGTCGTTAAG
















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|149073510|gb|EE161813.2|EE161813
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|76020464|gb|DT947634.1|DT947634
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|71443470|gb|DR824520.1|DR824520
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|60340573|gb|DN207546.1|DN207546
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|89246761|gb|DY618548.1|DY618548
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCNNNNNNNCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|211475623|gb|FL459214.1|FL459214
EST:     TCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: TCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|74237187|gb|DT645101.1|DT645101
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|60353293|gb|DN220266.1|DN220266
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|71770343|gb|DR968280.1|DR968280
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|37374830|gb|CF623807.1|CF623807
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|60356243|gb|DN223216.1|DN223216
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|5607779|gb|AI901446.1|AI901446
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|211034172|gb|FL478448.1|FL478448
EST:     GAAATCGGTCGACAG                         GGTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCCGGA
genomic: GAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|71314190|gb|DR793709.1|DR793709
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|148986505|gb|EE030255.2|EE030255
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|18164881|gb|BM334720.1|BM334720
EST:     ATTTCTCCATCAAAAAGGCATCTCGGTTGGTGAAAGGAGTCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|71761831|gb|DR959768.1|DR959768
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|60394000|gb|DN226870.1|DN226870
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|78088594|gb|DV516987.1|DV516987
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCNNNNNNNCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|14243604|gb|BG841264.2|BG841264
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
EST: gi|93282965|gb|EB675229.1|EB675229
EST:     ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAG                         GTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA
genomic: ATTTCTCCATCAAAAAGGCATCTCAATTGGTGAAAGAAATCGGTCGACAGgtaaattcat ... ttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttacttcattagccaactatgttcttatctattatcaatttttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG
                                          ttttttt  CT-rich tract
                  aactatgttcttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattcatctaatagtttctttacttcattagccaactatgttcttatctattatcaatttttttaaatagGTTGCAACTGATCGATGCATCATGGCCATGCTTTTTCTCATTGTTGCTGGAGTCATAGCTATAATAATTGTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA