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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttgtttccgttcatgtgtttgggactattcatttacgtacagttttccataacaacaaagcttgcttcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG

Basic information

species Oryza sativa
transcript LOC_Os12g01390.1
intron # 28
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 26
gtatcttgt---ttccgttcatgtgtttgggactattcatttacgtacagttttccataacaacaaagctt------------gcttcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
|||  | ||   ||| || |||||   ||      |  |||||| |||||||| |||||  ||||   ||              ||   || |||||||||||| || ||||| |||||||| |||||  |||||||||||| ||| || || ||||| |||| ||| || || |||||||| || ||||| ||||
gtacgtagtaatttctgtccatgttcgtgccgacgtctatttacatacagtttaccatagtaacatctctactgtgctatgtgactgtgtgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCCAAGGAGAAGGAGGAGAAAGACCTTG

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM2G115138_T01 (Zea mays), 3'ss of exon 12
gtatcttgt---ttccgttcatgtgtttgggactattcatttacgtacagttttccataacaacaaagctt------------gcttcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
|||  | ||   ||| || |||||   ||      |  |||||| |||||||  |||||  ||||   ||              ||   || |||||||||||| || ||||| |||||||| |||||  |||||||||||| ||| || || ||||| |||| ||| ||||| |||||||| || ||||| ||||
gtacgtagtaatttctgtccatgttcgtgccgacgtctatttacatacagtta-ccatagtaacatccctactgtgctatgtgactgtgtgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 5
gtatcttgtttccgttcatgtgtt-tgggactattcatttacgtacagttttccataacaacaaagcttgcttcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
||| |||  ||| || ||| | |   ||   | ||  |||| ||| | ||| | ||   ||||   | |||| | |||||||||||| || || ||||| |||||||| |||||  ||||||||||||| ||||| ||||||||||||| ||| |  ||||||||||| || ||||||||||
gtaacttacttctgtccatatctgacggtgatgtttgtttatgtataatttactatggtaacatc-catgctgcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTG

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 13
gtatcttgt---ttccgttcatgtgtttgggactattcatttacgtacagttttccataacaacaaagcttgcttcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
|||  | ||   ||  || |||||    |      |  |||||| |||||||| |||||  ||||   | | ||   || |||||||||||| || ||||| |||||||| |||||  |||||||||||| ||| || || ||||| |||| ||| ||||| |||||||| || ||||| ||||
gtacgtagtaatttttgtccatgttcgcgccgacgtctatttacatacagtttaccatagtaacatc-cctactatgtgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 5
----gtatcttgtttccgttcatgtgtttgggactattcatttacgtacagttttccataacaacaaagcttg--cttcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
     || ||| |||| |  | |   | |||   | ||  ||||| || ||||| | ||   || ||        || | |||||||||||| || || ||||| |||||||| |||||  ||||||||||||  || || ||||||||||||| ||| || ||||||||||| || ||||||||||
gtaactaacttatttctgcccgtacctgtggtgatgtttgtttacatatagtttactatggtaataacatccatcctgcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATCGAGTCACAGAATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTG

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 8
gtatcttgt---ttccgttcatgtgtttgggactattcatttacgtacagttttccataacaacaaagctt------------gcttcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
|||  | ||   ||| || |||||   ||      |  |||||| || ||||  |||||  ||||   ||              ||   || |||||||||||| || ||||| |||||||| |||||  |||||||||||| ||| || || ||||| |||| ||| ||||| |||||||| || ||||| ||||
gtacgtagtaatttctgtccatgttcgtgtcgacgtctatttacatatagtta-ccatagtaacatccctactgtgctatgtgactgtgtgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 13
gtatcttgt---ttccgttcatgtgtttgggactattcatttacgtacagttttccataacaacaaagct--tgcttcatgtg----------cagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
|||  | ||   ||| || |||||    |      |  | |||| |||||||  |||||  ||||   ||  ||    |||||          ||||||||||| || ||||| |||||||| |||||  |||||||||||| ||| || || ||||| |||| ||| ||||| |||||||| || ||||| ||||
gtacgtagtaatttctgtccatgttcgcgccgacgtctacttacatacagtta-ccatagtaacatccctactgtgctatgtgactgtctgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 28
-------gtatcttgtttccgttcatgtgtttggga-----ctattcatt-------tacgtacagttttccataacaacaaagcttgcttcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
       || |  |    || | |||     ||  |     ||||| |||       ||   | || ||||  | |  |  |   ||  |     || |||| ||||| ||||||||  |||| || ||||| |||||||||||||  |||||| |||| |||||||| | |||||||||| | |||||||| ||| | |
agttattgtcttctccagccttccattgagctgaaatgaatctatttattgccatcttatccagaggtttctctcatcattattttttttggggttgtagTTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATTGAAGCACAAAATGAAGTGAAGGCTAAAGAGCAAGAAGAAAAGGATGTAG

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|29663094|gb|CB659369.1|CB659369
EST:     TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAG                         TTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
genomic: TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtt ... tcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
EST: gi|29624231|gb|CB629242.1|CB629242
EST:     TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAG                         TTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
genomic: TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtt ... tcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
EST: gi|25800929|gb|CA756890.1|CA756890
EST:     GCATGAATG-ACAAACATGGT-GACTNTGCATTCCCCCTATCTGTTACAG                         TTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
genomic: GCATGGATGAAC-AACATGGTGGACTTTGCATT-CCCCTATCTGTTACAGgtatcttgtt ... tcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT

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: 72 (upstream exon), 75 (downstream exon)
Score: 191

TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtt ... tcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggactattcatttacgtacagttttccataacaacaaagcttgcttcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
                         ccataac  putative branch site (score: 191)
                                       cttgcttc  putative PPT
     attcattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcttgtttccgttcatgtgtttgggactattcatttacgtacagttttccataacaacaaagcttgcttcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA