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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatattgagatgacaaaattagaaactttaaccaggcaactcgacattctttgtaggctgactgtttttttttttttgttttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACGGCAAGTTGGTGGGGGCTAAATAACTGGATACCCATGTTTGATGTAGTAT

Basic information

species Oryza sativa
transcript LOC_Os07g27930.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g27930.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G29520.1 (Glycine max), 3'ss of exon 5
gtgagatattgag-atgaca-aaattagaaa----ctttaaccaggc------------aactcgacat--tctttgtaggctgactgtt---tttttttttttgttttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACGGCAAGTTGGTGGGGGCTAAATAACTGGATACCCATGTTTGATGTAGTAT-
|| |    |||   || | | || |||| ||     |||  |  |||            |  | || |   || |   |  |||||||||     |||||||     ||     |||||||| || |||||||||||||| || ||||| || |||||||||||  ||||||| ||||| |  | | | | || |    || || ||  |  |  | 
gtaaatacttggccattatacaagttaggaagttcttttttcttggctgggggaggttaaggttgataacatcatgccatactgactgttaatcatttttttgcaaatttctccagCTATGAAGATTGGGGAGTTGATGAACTGATTGTGGAAGACTCCTGGAAGAGGCAAGTGGGTGGTGATTGA-TGATTGAACTGACAGGTGTGGGGAGGAGTA

upper sequence: LOC_Os07g27930.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G51940.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagatattgagatgacaaaattagaaactttaaccaggcaactcgacattctttgtaggctgactgtttttttttttttgttttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACGGCAAGTTGGTGGGGGCTAAATAACTGGATACCCATGTTTGATGTAGTAT
|||||| ||||   |||     ||| |   ||          ||| ||  |  | | |   ||      ||  || |  ||    ||||| || |  ||||| |||||||||||||| || || || || ||||| |||||||| ||||||||||| |  | |  | |||   |   |    |     | || 
gtgagagattgcattga---gcttatattattctcttcactcacttgatctcttcttt--tcttgtgacttacttatgatt--cctgaaacagTTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGGAAACGTCAAGTTGGTGGTGATTGATAATCTGACCAGAGACAAATCGACAAATAC
















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|88506017|gb|CI433523.1|CI433523
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|89168501|gb|CI038855.1|CI038855
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|89168685|gb|CI038537.1|CI038537
EST:     AGAGCACGCAAGATCCCTTTCACGATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|58590685|gb|CF988993.1|CF988993
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|88435819|gb|CI513958.1|CI513958
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|33659391|gb|CF282004.1|CF282004
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|88958855|gb|CI381658.1|CI381658
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|55409572|gb|CV721948.1|CV721948
EST:     AGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|88286132|gb|CI515256.1|CI515256
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|88259548|gb|CI363841.1|CI363841
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|88506168|gb|CI433674.1|CI433674
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|88555714|gb|CI485991.1|CI485991
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTNTAAAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|88419886|gb|CI516335.1|CI516335
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|86867542|gb|CI337921.1|CI337921
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|38476890|gb|CF961023.1|CF961023
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|88541223|gb|CI468481.1|CI468481
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|13165597|gb|AU174394.1|AU174394
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|88549482|gb|CI479375.1|CI479375
EST:     AGAGCACCCAANATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGANTTGATGAGCTCATTGTAGAGGACTCCTGGAAACC
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
EST: gi|88992556|gb|CI035639.1|CI035639
EST:     AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAG                         CTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACG

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: 34 (upstream exon), 50 (downstream exon)
Score: 37

ATTGCCATGAAAGAATTGAGAGCACGCAAGATCCCTTTCACAATCAGGCGGTATTTACCTGATGGAAGgtgagatatt ... tttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACGGCAAGTTGGTGGGGGCTAAATAACTGGATACCCATGTTTGATGTAGTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaactcgacattctttgtaggctgactgtttttttttttttgttttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACGGCAAGTTGGTGGGGGCTAAATAACTGGATACCCATGTTTGATGTAGTAT
                     ggctgac  putative branch site (score: 37)
                           ctgttttttttttttt  CT-rich tract
                          actgtttttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatattgagatgacaaaattagaaactttaaccaggcaactcgacattctttgtaggctgactgtttttttttttttgttttgaaatagCTATGAGGACTGGGGAGTTGATGAGCTCATTGTAGAGGACTCCTGGAAACGGCAAGTTGGTGGGGGCTAAATAACTGGATACCCATGTTTGATGTAGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG