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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacttaattaattcattaattaattgccatttctagagctaagagcacctgcatctgcatgtggtgattaattactttggaattagtaattagttgctcatggtgattgattcctgaattgattgattgattgattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAAATGACGAGGTCAAAAGCCATCTTCAG

Basic information

species Oryza sativa
transcript LOC_Os07g02800.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g02800.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G173882_T01 (Zea mays), 3'ss of exon 3
gtacacttaattaattcattaattaattgccatttctagagctaagagcacctgcatctgcatgtggtgattaattactttggaattagtaattagttgctcatggtgattgattcctgaattgattgat---tgattgattg---tgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAAATGACGAGGTCAAAAGCCATCTTCAG
||   | |   |  ||||      ||||     ||   |   |  |    ||||||   || |||  | |   | |   |||      ||| |||| | |  |  ||     |||   || || ||| ||   ||||||  ||   |||||||||||| |||||||| ||||||||||||||||||||||| || || ||||| ||||| || |||||||| ||||||
gtgagccttgctc-ttcagatgcaaattatttcttgccggttttgggcggcctgca---gcgtgttcttacctacttgcttgcctgccgta-ttagatacgtagagttgg-aattaacgagttcattcatgtctgattgtctgcactgcagTTGCCACCCCAAAGCAGATCAGGGAGCTGATGAAGGTGGACGGCCTCACAAACGACGAAGTGAAAAGCCACCTTCAG

upper sequence: LOC_Os07g02800.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S83_100V6.1 (Physcomitrella patens), 3'ss of exon 4
gtacacttaattaattcattaattaattgccatttctagagctaagagcacct-gcatctgcatgtggtgattaattactttggaattagtaattagttgctcatggtgattgattcctgaattgattgattgattgattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAAATGACGAGGTCAAAAGCCATCTTCAG
                                | |||    |      | ||| |||| |   | ||||| ||    |  ||||| |      | |     |||   | | |||  |  |   ||          || ||||||||||||||| |||||||||||  | |||||||||||||| || || || || || ||||| || || |||||||| |||
------------------------------tttctctgtgtcggcattctccttgcattttgttctggtgttt----atgttggattcgaacttcacaaattcaacttcactga--cacgggctg----------tggttgtgcagTTGCCACGCCAAAGCAAATACGCGAGCTGATGAAGGTCGACGGCCTTACCAACGACGAAGTGAAGAGCCATCTGCAG

upper sequence: LOC_Os07g02800.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ37607 (Selaginella moellendorffii), 3'ss of exon 3
gtacacttaattaattcattaattaattgccatttctagagctaagagcacctgcatctgcatgtggtgattaattactttggaattagtaattagttgctcatggtgattgattcctgaattgattgattgattgattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAAATGACGAGGTCAAAAGCCATCTTCAG
                                                                                ||  |  |||||||    || |  | | |    ||| | ||    |    |  |||||    ||||||| ||||||||||||||| | ||||| |||||||| ||||| || ||||| || || || |||||||| || |||
-------------------------------------------------------------------------------gtgcgac-agtaattcaa-gcgctcgatcaaaagttcttaaaggtttcttcttcttgatc---cagTTGCAACTCCAAAGCAAATCCGAGAGCTCATGAAGGTAGATGGTCTTACAAACGATGAAGTAAAAAGCCACCTCCAG

upper sequence: LOC_Os07g02800.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ15083 (Selaginella moellendorffii), 3'ss of exon 3
gtacacttaattaattcattaattaattgccatttctagagctaagagcacctgcatctgcatgtggtgattaattactttggaattagtaattagttgctcatggtgattgattcctgaattgattgattgattgattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAAATGACGAGGTCAAAAGCCATCTTCAG
                                                               |||  ||  | ||| | || | | |          || |  | |      ||| | ||    |    |  |||||    ||||||||||||||||||||||| | || || |||||||| ||||| || ||||| || || || |||||||| || |||
---------------------------------------------------------------gtg-cgac-agttattctgaattcaa---------gcgctcgatcgaaagttcttaaaggtttcttcttcttgatc---cagTTGCCACTCCAAAGCAAATCCGAGAACTCATGAAGGTAGATGGTCTTACAAACGATGAAGTAAAAAGCCACCTCCAG

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|29684475|gb|CB680750.1|CB680750
EST:     CCTCCACCGCAAGTTCGTCGCCGCCTTGCAGCAACTCGGTGGCCCTCAAG                         TTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
genomic: CCTCCACCGCAAGTTCGTCGCCGCCTTGCAGCAACTCGGTGGCCCTCAAGgtacacttaa ... gattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
EST: gi|4714655|gb|AU055772.1|AU055772
EST:     CCGCCTTGCCAGCAAACTCGNTGCCCCTCAAG                         T
genomic: CCGCCTTG-CAGC-AACTCGGTGGCCCTCAAGgtacacttaa ... gattgtgcag-
EST: gi|4714655|gb|AU055772.1|AU055772
EST:     CCGCCTTGCCAGCAAACTCGNTGCCCCTCAAG                         T
genomic: CCGCCTTG-CAGC-AACTCGGTGGCCCTCAAGgtacacttaa ... gattgtgcag-
EST: gi|29686226|gb|CB682501.1|CB682501
EST:     TGCAGCAACTCGGTGGCCCTCAAG                         TTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
genomic: TGCAGCAACTCGGTGGCCCTCAAGgtacacttaa ... gattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
EST: gi|29659108|gb|CB655383.1|CB655383
EST:     CCTCCACCGCAAGTTCGTCGCCGCCTTGCAGCAACTCGGTGGCCCTCAAG                         TTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
genomic: CCTCCACCGCAAGTTCGTCGCCGCCTTGCAGCAACTCGGTGGCCCTCAAGgtacacttaa ... gattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
EST: gi|29661590|gb|CB657865.1|CB657865
EST:     CGCAAGTTCGTCGCCGCCTTGCAGCAACTCGGTGGCCCTCAAG                         TTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
genomic: CGCAAGTTCGTCGCCGCCTTGCAGCAACTCGGTGGCCCTCAAGgtacacttaa ... gattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
EST: gi|29674102|gb|CB670377.1|CB670377
EST:     CCTCCACCGCAAGTTCGTCGCCGCCTTGCAGCAACTCGGTGGCCCTCAAG                         TTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
genomic: CCTCCACCGCAAGTTCGTCGCCGCCTTGCAGCAACTCGGTGGCCCTCAAGgtacacttaa ... gattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
EST: gi|87029253|gb|CI276521.1|CI276521
EST:     CCACCGCAAGTTCGTCGCCGCCTTGCAGCAACTCGGTGGCCCTCAAG                         TTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
genomic: CCACCGCAAGTTCGTCGCCGCCTTGCAGCAACTCGGTGGCCCTCAAGgtacacttaa ... gattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
EST: gi|29675135|gb|CB671410.1|CB671410
EST:     CAAGTTCGTCGCCGCCTTGCAGCAACTCGGTGGCCCTCAAG                         TTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
genomic: CAAGTTCGTCGCCGCCTTGCAGCAACTCGGTGGCCCTCAAGgtacacttaa ... gattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
EST: gi|86823299|gb|CI256309.1|CI256309
EST:     GCCGCCTTGCAGCAACTCGGTGGCCCTCAAG                         TTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA
genomic: GCCGCCTTGCAGCAACTCGGTGGCCCTCAAGgtacacttaa ... gattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAA

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: 65 (upstream exon), 54 (downstream exon)
Score: 7

GCGCAGCAGCAGCAGCAGGCGAGGAAGACGAGGCGGTGCTGGTCGCCGGACCTCCACCGCAAGTTCGTCGCCGCCTTGCAGCAACTCGGTGGCCCTCAAGgtacacttaa ... gattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAAATGACGAGGTCAAAAGCCATCTTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattagttgctcatggtgattgattcctgaattgattgattgattgattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAAATGACGAGGTCAAAAGCCATCTTCAG
                                         gattgat  putative branch site (score: 7)
                             aattgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacttaattaattcattaattaattgccatttctagagctaagagcacctgcatctgcatgtggtgattaattactttggaattagtaattagttgctcatggtgattgattcctgaattgattgattgattgattgtgcagTTGCCACTCCAAAGCAAATCAGGGAGCTGATGAAGGTGGATGGACTGACAAATGACGAGGTCAAAAGCCATCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA