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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactagtttacttgacattattcctgcctttcattttcttatcacgtcctaatcatatattgcctttgagttctatatttttctaatgaaaactttgaactccacatcaaagCTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG

Basic information

species Oryza sativa
transcript LOC_Os11g03730.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G393002_T01 (Zea mays), 3'ss of exon 17
gtactagtttacttgacattattcctgcctttcattttcttatcacgtcctaatcatatattgcctttgagttctatatttttctaatgaaaac-tttgaactccacatcaaagCTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG
                              | ||   ||  || ||    |  |||||   |  ||||    || ||  |   ||||| |  || |||||| ||||  | |||||||||||||||  | |||||||||||||||||||| ||||||||||
-----------------------------gtacaagatca-attacactgtt-tcatactctctcttttttctc-atcatcacctaattatcacatttgaaatccatgtaaaagCTTTCTGAGGACATAGGTGCTGCCCCAATCTGGGTATTCAACAATG

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 8
gtactagtttacttgacattattcctgcctttcattttcttatcacgtcctaatcatatattgcctttgagttctatatttttctaatgaaaactttgaactccacatcaaagCTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG
|| | ||||||     | |   | |   ||||| ||  ||  |   ||||| |              |||   | | | ||          |||| |||| || |||||||||||| | ||||| |||||| |||  ||||||||||| ||||||||||
gtgccagtttatactgcttctgttcgagctttccttccctgttggtgtcctcac-------------tga---caacaatt----------aactctgaaatctacatcaaagCTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G006130_T03 (Zea mays), 3'ss of exon 8
gtactagtttacttgacattattcctgcctttcattttcttatcacgtcctaatc-atatattgcctttgagttctatatttttctaatgaaaactttgaactccacatcaaagCTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG
                 || | | |   |    |     |||    |    | |  || ||||    ||   |   ||      ||||  |  |  ||||| || || ||||||||| | ||||| ||||||||||||||||| ||||| ||||||||||
--------------attatgagttccttcaggtaccagtttacactgcttcactttatttatttttctttcctatcatgaccccctaagtattatattgaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 8
gtactagtttacttgacattattcctgcctttcattttcttatcacgtcctaatcatatattgcctttgagttctatatttttctaatgaaaactttgaactccacatcaaagCTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG
|||| |||||||        | | || |  || ||||  || ||   | |  |||||      ||  | |||  ||||||                 ||| || || ||||||||| | ||||| ||||||||||||||||||||||| ||||||||||
gtaccagtttac--------actgcttcactttatttatttttct--ttcctatcatg----acccctaagtattatatt-----------------gaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G006130_T02 (Zea mays), 3'ss of exon 8
gtactagtttacttgacattattcctgcctttcattttcttatcacgtcctaatcatatattgcctttgagttctatatttttctaatgaaaactttgaactccacatcaaagCTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG
                             |  || |||   |   | | |   | || ||||    ||   |   ||      ||||  |  |  ||||| || || ||||||||| | ||||| ||||||||||||||||| ||||| ||||||||||
----------------------------gtaccagtttac-actgc-ttcactttatttatttttctttcctatcatgaccccctaagtattatattgaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG

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|29672785|gb|CB669060.1|CB669060
EST:     TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAATTTCTCCAG                         CTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAATTTCTCCAGgtactagttt ... cacatcaaagCTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG
EST: gi|29644765|gb|CB649772.1|CB649772
EST:     TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAATTTCTCCAG                         CTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAATTTCTCCAGgtactagttt ... cacatcaaagCTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG
EST: gi|29646541|gb|CB651548.1|CB651548
EST:     TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAATTTCTCCAG                         CTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTNCA-CAATG
genomic: TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAATTTCTCCAGgtactagttt ... cacatcaaagCTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTT-CAACAATG
EST: gi|29636288|gb|CB641297.1|CB641297
EST:     TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATTAATTTTTCCAG                         CTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAATTTCTCCAGgtactagttt ... cacatcaaagCTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG

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: 71 (upstream exon), 46 (downstream exon)
Score: 27

GAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAATTTCTCCAGgtactagttt ... cacatcaaagCTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgcctttgagttctatatttttctaatgaaaactttgaactccacatcaaagCTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG
                       ttctaat  putative branch site (score: 27)
                tatatttttctaatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactagtttacttgacattattcctgcctttcattttcttatcacgtcctaatcatatattgcctttgagttctatatttttctaatgaaaactttgaactccacatcaaagCTTTCTGAGGATCTGGGTGCTGCCCCAATCTGGGTGTTCAACAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC