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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcttttttcagtaatctgattgatctccatattattctagtcactattatctgttggcatcacaccgatgcttgacatttttgtaattatattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCTCGAGGAGAGATTGTCATTGGTGGTCCCAATGTAACTAAAGGCTATTTCA

Basic information

species Oryza sativa
transcript LOC_Os12g07110.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 8
atcttttttcagtaatctgattgatctccatattattctagtcactattatctgttggcatcacaccgatgct-------tgacatttttgtaattatattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCTCGAGGAGAGATTGTCATTGGTGGTCCCAATGTAACTAAAGGCTATTTCA
        |  |  |||| ||  ||     |   | |  |     | ||| |||||| | || ||| | | ||       |||||| |  |  | | |||| |  || ||||||||||| | || ||||||||||| ||   ||| |  ||||||||||| ||||| ||||||||||| ||||| ||| ||||||||||||||||||
-----cactgggatatcttatctattcttgtgacagtgaatgagttctta-ctgttgacctcccacagttcctgacttcctgacatatcagccactgtatt-tttagTTGATTGACTGGCCTGAGGGTGGATACTTGACTGCTGATTTACCAATGCCTCGGGGAGAAATTGTCATTGGAGGTCCAAATATAACTAAAGGCTATTTCA

upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 7
atcttttttcagta-atctgattgatctccatattattctagtcactattatctgttggcatcacaccgatgcttgacatttttgtaattatattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCTCGAGGAGAGATTGTCATTGGTGGTCCCAATGTAACTAAAGGCTATTTCA
 |  |  || | || || | ||  | |||||||  ||| ||  | | |  |    ||   |  |||   |||||   | |||||         |    ||||| ||||||||| | ||||||||||| | ||| |||||||| |||||| | ||||| || ||||| ||||||||||| ||||| |||   || || ||||
gtagtaattgattagatgtaatccacctccatac-attttaacctcaaggaatatttacta--acataaatgct---ccttttt---------tccctcagCTAATTGACTGGCCCGAAGGTGGATATTCAACCAGTGACTCACCAATGGCGCGAGGTGAAATTGTAATTGGTGGTCCAAATGTCACTCTTGGATACTTCA

upper sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 9
-------atctttt-ttcagtaatctgattgatctccatattattctagtcactattatctgttggcatcacaccgatgcttgacatttttgtaattatattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCTCGAGGAGAGATTGTCATTGGTGGTCCCAATGTAACTAAAGGCTATTTCA
       ||||| |   | ||  |    |||||      |||    ||       |||    ||   |||| |   |    | |  |||||     | | ||   ||| ||||  | ||| | || ||||| || |||||||||||    ||||||||||||||||| || |||||||||||||| ||||| |||   || |||||||
cgagaaaatcttataccctgttgtaattttgattaatgcatttcaatatatggccttactaattctaatcatattaaga--taatgttttt----ctctgtt--tcagTTGATAAATTGGCCTGAGGGTGGGTATTTAACAAGTGATAAACCAATGCCTCGAGGAGAAATAGTCATTGGTGGTCCAAATGTTACTGTTGGATATTTCA

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|29669841|gb|CB666116.1|CB666116
EST:     ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAG                         CTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGC
genomic: ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttg ... tattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGC
EST: gi|29614988|gb|CB620001.1|CB620001
EST:     ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAG                         CTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCT
genomic: ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttg ... tattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCT
EST: gi|29675500|gb|CB671775.1|CB671775
EST:     ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAG                         CTGATTGACTGGTCAGAAGGTGGATACTTAACAAGAAAGTCCCCAATGCCT
genomic: ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttg ... tattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCT
EST: gi|58030548|gb|CX728091.1|CX728091
EST:     ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACAATAAG                         CTGATTGACTGGTCAGAAGGTGGATACTTAACAAGAGAGTCCCCAATG
genomic: ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttg ... tattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATG
EST: gi|29672201|gb|CB668476.1|CB668476
EST:     ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACAATGAG                         CTGATTGACTGGTCAGAAGGTGGAT
genomic: ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttg ... tattatccagCTGATTGACTGGTCAGAAGGTGGAT
EST: gi|29614945|gb|CB619958.1|CB619958
EST:     ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATGAAG                         CTGATTGACTGGTCAGAAGGTGGATACTTAACAAA-GAGTCCCCAATGCCT
genomic: ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttg ... tattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCT
EST: gi|13420751|gb|AU174841.1|AU174841
EST:     ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAG                         CTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGC
genomic: ACCCATCTGTTGGTCGCGTTGGTGCTCCACTACCTTGTTCGTACATTAAGgtaagttttg ... tattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattatctgttggcatcacaccgatgcttgacatttttgtaattatattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCTCGAGGAGAGATTGTCATTGGTGGTCCCAATGTAACTAAAGGCTATTTCA
                         gcttgac  putative branch site (score: 4)
                           ttgacatttttgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcttttttcagtaatctgattgatctccatattattctagtcactattatctgttggcatcacaccgatgcttgacatttttgtaattatattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCTCGAGGAGAGATTGTCATTGGTGGTCCCAATGTAACTAAAGGCTATTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG