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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagatgcttgttcttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgacagGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG

Basic information

species Oryza sativa
transcript LOC_Os07g30840.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G152100_T01 (Zea mays), 3'ss of exon 4
gtcagatgcttgtt-cttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgac--agGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG----
|| |||||||||   | |  |  | |||  |         |||| | || ||| | ||||||     ||  | |   ||| | | |    |||||||||||||| ||||||| |||||||||||||| ||||| ||||| |||||||| |  |||||||||||    
gtaagatgcttgcagcctgtatctgcatcat---------cattatctatctgtccaatgatatttttatctgcatactgcattcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGAGCAGCTAAACAACATGATAGAGATCTTATCTGACTGGTTT

upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G152100_T02 (Zea mays), 3'ss of exon 3
gtcagatgcttgtt-cttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgac--agGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG-----------------------------
|| |||||||||   | |  |  | |||  |         |||| | || ||| | ||||||     ||  | |   ||| | | |    |||||||||||||| ||||||| |||||||||||||| ||||| ||||| |||||||| |  |||||||||||                             
gtaagatgcttgcagcctgtatctgcatcat---------cattatctatctgtccaatgatatttttatctgcatactgcattcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGAGCAGCTAAACAACATGATAGAGATCTTATCTGACTGGTTTGTATGCTTATTTAAGAAATTTTCTA

upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G152805_T01 (Zea mays), 3'ss of exon 5
gtcagatgcttgttcttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgac--agGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG----
|| |||||||||        ||  |  | |     |  ||||| | || ||| | ||||||     ||  | |   ||| | | |    |||||||||||||| ||||||| |||||||||||||||||||| || || |||||||| |  |||||||||||    
gtaagatgcttgc-------agc-ctgtatctgcagcatcattatctatctgtccaatgatatttttacctccatactgcattcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAATAACATGATAGAGATCTTATCTGACTGGTTT

upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G171745_T04 (Zea mays), 3'ss of exon 5
gtcagatgcttgtt-cttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgac--agGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG
|  |||||||||   | |  |  | ||   |    | ||||  ||| ||  ||  || |  |      | ||| | |||| | |      |||||||||||||| ||||||| |||||||||||||||||||| || || |||||||| || || ||||| ||
gcaagatgcttgcggcctgtatctgcagcatc---gttttctctgtctaa-tgataacttttttatgaacattttctctgcattcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG

upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G027551_T01 (Zea mays), 3'ss of exon 3
gtcagatgcttgttcttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgac--agGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG-----------------------------
|| |||||||||        ||  |  | |     |  ||||| | || ||  | ||||||     ||  | |   ||| | | |    |||||||||||||| ||||||| |||||||||||||||||||| ||||| |||||||| |  |||||||||||                             
gtaagatgcttgc-------agc-ctgtatctgcagcatcattatctatctatccaatgatatttttatctgcatactgcattcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGGTTTGTATGCTTATTTAAGAAATTTTCTA

upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G085670_T04 (Zea mays), 3'ss of exon 5
gtcagatgcttgttcttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgac--agGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG
|| |||||||||        ||  |  | |     | |||||| | || ||| | ||||||     || || |   ||| | | |    |||||||||||||| ||||||| |||||||||||||||||||| ||||| |||||||| |  |||||||||||
gtaagatgcttgc-------agc-ctgtatctgcagcttcattatctatctgtccaatgatatttttatatgcatactgcattcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG

upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G115277_T01 (Zea mays), 3'ss of exon 5
gtcagatgcttgttcttacaagtacattgttcatggtttcattgtttagctggcaaatgatcccc---ctaaattctgtctgtacttgacagGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG
|| |||||||||        ||  |  | |     |  ||||| | || ||| | ||||||       ||  || |||  |    ||   |||||||||||||| ||||||| |||||||||||||||||||| || || |||||||                
gtaagatgcttgc-------agc-ctgtatctgcagcatcattatctatctgtccaatgatattttatctgcatactgcattcgttt--tagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAATAACATGATAG----------------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgacagGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG
                             ccctaaa  putative branch site (score: 3)
      attgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagatgcttgttcttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgacagGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA