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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttagtttatgttgtacatgctgttgattgttgaaaggttcatagaaaattgtccctgattgacacctcttacttgacccttctttcttgtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATTGGTGATCAGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGC

Basic information

species Oryza sativa
transcript LOC_Os04g37660.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g37660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G044382_T01 (Zea mays), 3'ss of exon 4
agttagtttatgttgtacatgctgttgattgttgaaaggttcatagaaaattgtccctgattgacacctcttacttgaccctt-----ctttcttgtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATTGGTGATCAGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGC
     |   || ||  | | | | |   ||   |     ||  | |     |     ||||  |  |||  |  |||| ||||     |||| || ||||| |||||||| || |||||||||||||| ||||| || ||||| |||||||| ||||||||||||||||||||||||||||| ||||| || |||||||||||||
----tggacatcttccataggttttcttttagagtcctattttttggtttgtagatgtgatccatgccttct-tttgatccttagttccttttttatccatccagATTGGTCCCCTTAGATGTTGGCCAGGTGGTTTATGCCTCTCAAGATCGATTGGTGATCAGGATGTAGGTGAATTTATTATTCCGGTTCCTTATGTGAAGC

upper sequence: LOC_Os04g37660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G015610_T02 (Zea mays), 3'ss of exon 4
---agttagtttatgttgtacatgctgttgattgttgaaaggttcatagaaaattgtccctgattgacacctcttacttgacccttctttcttgtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATTGGTGATCAGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGC
   |  |    || ||| | | |   |     | |     ||||  |||     ||   |  |    |   |  | ||| |  | | ||| || ||||| |||||||| || |||||||||||||| |||||  | ||||| |||||||| |||||||||||||| |||||||||||||||||||| || |||||||||||||
gacatcttccataggttttccttttagagtcctatcttttggtttgtaggtg--tgattcacaccctcttttgatcctttattccttttt-ttatccatccagATTGGTCCCCTTAGATGTTGGCCAGGTGGTCTATGCCTCTCAAGATCGATTGGTGATCAGGACGTAGGTGAATTTATCATTCCGGTTCCTTATGTGAAGC

upper sequence: LOC_Os04g37660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G04210.1 (Glycine max), 3'ss of exon 4
---agttagtttatgttgtacatgctgttgattgttgaaaggttcatagaaaa-ttgtccctgattgacacctcttacttgacccttctttcttgtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATTGGTGATCAGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGC
   | || | ||||  |     |||  || | |  |      |  | |  ||| |||    ||| |   |  |  | | ||||     ||  |  |   |  || |||| ||  | ||||||||||||||||||||||| || ||| |||| |||||||||  |||||| |||||||||||  | || || ||  |||| ||||
gatatttggattatcatcctt-tgcaatttactaatattctctctagaagaaacttgcatttgagttgta--ttatgcctgactaga-ttaatgatatttgtagGTTGGTCCTTTGAGATGTTGGCCTGGTGGCTTGTGTCTCTCACGATCCATTGGTGATATGGATGTTGGTGAATTTATTGTCCCTGTACCACATGTAAAGC

upper sequence: LOC_Os04g37660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G36150.2 (Glycine max), 3'ss of exon 4
---agttagtttatgttgtacatgc-tgttgattgttgaaaggttcatagaaaattgtccctgat--tgacacctcttacttgacccttctttcttgtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATTGGTGATCAGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGC
     || ||||| ||| |  |  | ||||   | |   ||  ||  |  |||| |||   ||||  | | |   || ||| ||   ||  ||  | ||   | || |||| ||  | ||||||||||||||||| ||||| || ||| |||| ||||| |||  |||| | |||||||||||  | || || || ||||| ||||
acacttttgtttaggttttgtactcatgttttgtttaccaatattattgaaaaagtgtttatgatattaatatgcctgactaga---ttaatttgtatc---aaagGTTGGTCCTTTGAGATGTTGGCCTGGTGGTTTGTGTCTCTCACGATCTATTGGAGATATGGATATTGGTGAATTTATTGTACCTGTCCCGTATGTAAAGC

upper sequence: LOC_Os04g37660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G09020.1 (Glycine max), 3'ss of exon 5
agttagtttatgttgtacatgc--tgttgattgttga--aaggttca---tagaaaattgtccctgat--tgacacctcttacttgacccttctttcttgtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATTGGTGATCAGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGC
    | ||| |  | ||||  |  | | | ||||| |  ||  |||    ||||||| |||   ||||  | | |   || ||| ||    | ||| |||       || |||| ||  | ||||||||||||||||||||||| || ||| |||| ||||| |||  |||| | |||||||||||  | || || || ||||| ||||
---gattttgtactatacagaccatatggtttgtttaccaatattctctttagaaaagtgtttatgatactaatatgcctgactagattaatttttattga------agGTTGGTCCTTTGAGATGTTGGCCTGGTGGCTTGTGTCTCTCACGATCTATTGGAGATATGGATATTGGTGAATTTATTGTCCCTGTACCGTATGTAAAGC

upper sequence: LOC_Os04g37660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G04040.1 (Glycine max), 3'ss of exon 4
---agttagtttatgttgtacatgctgttgattgttgaaaggttcatagaaaa-ttgtccctgattgacacctcttacttgacccttctttcttgtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATTGGTGATCAGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGC
   | |||| |||| ||     |||  || | |  |      |  | |  ||| |||    ||| |   |  |  | | || |     ||  |  |   |  || |||| ||  | ||||||||||||||||||||||| || ||| |||| |||||||||  |||||| |||||||||||  | || || ||  | || ||||
gctatttagattatcttcctt-tgcaatttactaatattctctctagaagaaacttgcatttgagttgta--ttatgcctggctaga-ttaatgatatttgtagGTTGGTCCTTTGAGATGTTGGCCTGGTGGCTTGTGTCTCTCACGATCCATTGGTGATATGGATGTTGGTGAATTTATTGTCCCTGTACCACACGTAAAGC

upper sequence: LOC_Os04g37660.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
agttagtttatgttgtacatgctgttgattgttgaaaggttcatagaaaattgtccctg-attgacacctctta----cttgacccttctttcttgtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATTGGTGATCAGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGC
|  |    |||  ||       ||| || |||         |||||  || | ||  ||    | ||  |   |     ||||    |   |||| |   |  ||||||| || || |||||||||||||||||  |||| || |||||||| ||||| |||| |||||| || ||||  ||  |||| || |||||||| ||||
aactgtcatattgtggtagctttgtagaatgt-----aacacatagggaaatatctttgtgccgtcaaattgaagagttttgataactaaatcttatttttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC

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|29636845|gb|CB641854.1|CB641854
EST:     CAGAATGCGGAGGTGAAGTTGGAAGGCTAAATGTTGTCGGCGGAGCTGAG                         ATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATT
genomic: CAGAATGCGGAGGTGAAGTTGGAAGGCTAAATGTTGTCGGCGGAGCTGAGgtttttgctc ... gtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATT
EST: gi|40490361|gb|BX899888.1|BX899888
EST:     CAGAATGCGGAGGTGAAGTTGGAAGGCTAAATGTTGTCGGCGGAGCTGAG                         ATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCCATCAAGATCAATT
genomic: CAGAATGCGGAGGTGAAGTTGGAAGGCTAAATGTTGTCGGCGGAGCTGAGgtttttgctc ... gtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATT
EST: gi|27547836|gb|CA765984.2|CA765984
EST:     CAGAACGCGGAGGTGAAGTTGGAAGGCTAAATGTTGTCGGCGGAGCTGAG                         ATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATT
genomic: CAGAATGCGGAGGTGAAGTTGGAAGGCTAAATGTTGTCGGCGGAGCTGAGgtttttgctc ... gtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATT
EST: gi|58673154|gb|CK061840.1|CK061840
EST:     CAGAATGCGGAGGTGAAGTTGGAAGGCTAAATGTTGTCGGCGGAGCTGAG                         ATTGGGCCACTTAGATGTTGGCCTGGTGGCTTG
genomic: CAGAATGCGGAGGTGAAGTTGGAAGGCTAAATGTTGTCGGCGGAGCTGAGgtttttgctc ... gtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTG
EST: gi|58605846|gb|CK033879.1|CK033879
EST:     GGCTAAATGTTGTCGGCGGAGCTGAG                         ATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATT
genomic: GGCTAAATGTTGTCGGCGGAGCTGAGgtttttgctc ... gtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 64 (upstream exon), 65 (downstream exon)
Score: 29

GGTTGGACGTGTAACAGAATGCGGAGGTGAAGTTGGAAGGCTAAATGTTGTCGGCGGAGCTGAGgtttttgctc ... gtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATTGGTGATCAGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaattgtccctgattgacacctcttacttgacccttctttcttgtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATTGGTGATCAGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGC
                     cctcttacttgaccct  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttagtttatgttgtacatgctgttgattgttgaaaggttcatagaaaattgtccctgattgacacctcttacttgacccttctttcttgtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATTGGTGATCAGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC