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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtttctgcgaacttctccgtgcttttcttgtgtatatgagtaagtaacatttattggacacttgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG

Basic information

species Oryza sativa
transcript LOC_Os07g37740.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 8
-----------------gtattgtttctgcgaacttctccgtgcttttcttgtgtatatgagtaagtaacatttattggacacttgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
                   |||   |           ||     |||| |||| |  |    || ||||   ||  |||  |||||||||| ||||||||||| || |||||||||||||||||||||||| ||||| | 
gtattttatttgaaatctcattacattattttgtgcatctaccatttttttgtatgcacatataggtaatgcttgctggcaacttgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G448715_T02 (Zea mays), 3'ss of exon 8
-------------------gtattgtttctgcgaacttctccgtgcttttcttgtgtatatgagtaagtaacatttattggacacttgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG---------
                    |    ||  |  |  | ||| |    | |  |||| |  |||  || ||||  |||| |||  ||||||||||||||||||||||||| |||||||||||||||||||||||| ||||| ||         
gtaatttatttgaaatctcatcacattattttgtgcctctaccatatatctttgtatgcatggataggtaatgtttactggcaacttgttttgtagGACTGATAGTGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACTTGGTAAATATA

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G07480.1 (Glycine max), 3'ss of exon 8
---------------------gtattgtttctgcgaacttctccgtgcttttcttgtgtatatgagtaagta-acatttattggacacttgt-tttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
                       | |||   |||  | ||         |   |||  || |    | | |    |||| ||  |   || | ||||||||||||| ||||| ||||| ||||||| ||| |||||| ||||||||
ttcaatcctgcgcaatcaaacaaaatgtgcttgcatattttgatcattgtaatttggttacactcttgattttgaatttgttccattgttatatttgtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG

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|86430196|gb|CI082619.1|CI082619
EST:     CATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAG                         GACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
genomic: CATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAGgtattgtttc ... tgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
EST: gi|66923956|gb|CX110804.1|CX110804
EST:     GTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAG                         GACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
genomic: GTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAGgtattgtttc ... tgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
EST: gi|86429939|gb|CI082362.1|CI082362
EST:     TCGACCTCTGTATAATGCTATGAG                         GACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
genomic: TCGACCTCTGTATAATGCTATGAGgtattgtttc ... tgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
EST: gi|87027955|gb|CI276311.1|CI276311
EST:     ATAATGCTATGAG                         GACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
genomic: ATAATGCTATGAGgtattgtttc ... tgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
EST: gi|58683369|gb|CK072056.1|CK072056
EST:     GTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAG                         GACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
genomic: GTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAGgtattgtttc ... tgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
EST: gi|88966183|gb|CI013059.1|CI013059
EST:     GTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAG                         GACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
genomic: GTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAGgtattgtttc ... tgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG

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: 70 (upstream exon), 43 (downstream exon)
Score: 20

GCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAGgtattgtttc ... tgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgcttttcttgtgtatatgagtaagtaacatttattggacacttgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
                        aagtaac  putative branch site (score: 20)
                                           cttgtttt  putative PPT
                       taagtaacatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtttctgcgaacttctccgtgcttttcttgtgtatatgagtaagtaacatttattggacacttgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG