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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctattcattgttgatgactactgcaaattctttagttcctagtcttctagacgcatccaacatgtaattgagtggtgctctatttatcttcaatatagGTTGGACCAGCTGCGCAATCATCTGTCGCAGTTCACCAATCAGCTGCCCAACAATCAGTTTCATCTCAATCAGGAGAACCTTCTGCAGTTGCTATACCCT

Basic information

species Oryza sativa
transcript LOC_Os07g25710.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g25710.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G162409_T01 (Zea mays), 3'ss of exon 2
tgctattcattgt-tgatgactactgcaaattctttagttcctagtctt-ctagac-gcatccaacatgtaattgagtggtgctcta-tttatcttcaatatagGTTGGACCAGCTGCGCAATCATCTGTCGCAGTTCACCAATCAGCTGCCCAACAATCAGTTTCATCTCAATCAGGAGAACCTTCTGCAGTTGCTATACCCT
    ||  ||  | |  || |||   ||  ||  || |||   |   || ||  ||   |  |    | ||      |  |||  || ||| | ||  | ||||||||| | | ||| |||||||||   | ||||||||||||||||| |||||||| |||||||||||||||| |  ||||| |  |||||||    |||||
----atcaatcttgtattggctaggtcacttttctttgttataacctttactgcactatactctttgtttatagtctttatgcattaatttgtgtttcacatagGTTGGGCAACCTGTGCAATCATCCAACTCAGTTCACCAATCAGCTACCCAACAAACAGTTTCATCTCAATCTGTTGAACCGTTGGCAGTTGTGGCACCCT
















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|58669237|gb|CK057923.1|CK057923
EST:     ATGACTGGAAAGATATTGATAACACAGCTTGTACTGAAACTCAACCACAG                         GTTGGACCAGCTGCGCAATCATCTGTCGCAGTTCACCAATCAGCTGCCCC-
genomic: ATGACTGGAAAGATATTGATAACACAGCTTGTACTGAAACTCAACCACAGgtatgacagt ... ttcaatatagGTTGGACCAGCTGCGCAATCATCTGTCGCAGTTCACCAATCAGCTGCCCAA
EST: gi|29613089|gb|CB618102.1|CB618102
EST:     ATGACTGGAAAGATATTGATAACACAGCTTGTACTGAAACTCAACCACAG                         GTTGGACCAGCTGCGCAATCATCTGTCGCAG
genomic: ATGACTGGAAAGATATTGATAACACAGCTTGTACTGAAACTCAACCACAGgtatgacagt ... ttcaatatagGTTGGACCAGCTGCGCAATCATCTGTCGCAG
EST: gi|32948128|gb|BP184700.1|BP184700
EST:     ATGACTGGAAAGATATTGATAACACAGCTTGTACTGAAACTCAACCACAG                         GTTGGACCAGCTGCGCA
genomic: ATGACTGGAAAGATATTGATAACACAGCTTGTACTGAAACTCAACCACAGgtatgacagt ... ttcaatatagGTTGGACCAGCTGCGCA
EST: gi|55411384|gb|CV723760.1|CV723760
EST:     ATGACTGGAAAGATATTGATAACACAGCTTGTACTGAAACTCAACCACAG                         GTTGGACCAGCTGCGCAATCATCTGTCGCAGTTCACCAATCAGCTGCCCAA
genomic: ATGACTGGAAAGATATTGATAACACAGCTTGTACTGAAACTCAACCACAGgtatgacagt ... ttcaatatagGTTGGACCAGCTGCGCAATCATCTGTCGCAGTTCACCAATCAGCTGCCCAA
EST: gi|33380900|gb|CF196243.1|CF196243
EST:     ATGACTGGAAAGATATTGATAACACAGCTTGTACTGAAACTCAACCACAG                         GTTGGACCAGCTGCGCAATCATCTGTCGCAGTTCACCAATCAGCTGCCCAA
genomic: ATGACTGGAAAGATATTGATAACACAGCTTGTACTGAAACTCAACCACAGgtatgacagt ... ttcaatatagGTTGGACCAGCTGCGCAATCATCTGTCGCAGTTCACCAATCAGCTGCCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctagacgcatccaacatgtaattgagtggtgctctatttatcttcaatatagGTTGGACCAGCTGCGCAATCATCTGTCGCAGTTCACCAATCAGCTGCCCAACAATCAGTTTCATCTCAATCAGGAGAACCTTCTGCAGTTGCTATACCCT
                                  ctctatttatcttc  CT-rich tract
                                     tatttatcttcaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctattcattgttgatgactactgcaaattctttagttcctagtcttctagacgcatccaacatgtaattgagtggtgctctatttatcttcaatatagGTTGGACCAGCTGCGCAATCATCTGTCGCAGTTCACCAATCAGCTGCCCAACAATCAGTTTCATCTCAATCAGGAGAACCTTCTGCAGTTGCTATACCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG