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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccattgccatagagcttcactgttcattgtcatatatacaaactgacaaagtgttgtaaacctgtaatttctacttgatcatctaagactaagatgccacttcttagGTTCCAACAGGCTGGAAATTTTTTGGCAACCTAATGGATGCAGGAAAATTGTCTATTTGTGGAGAGGAAAGTTTTGGGACTGGATCTGATCACATCAGAG

Basic information

species Zea mays
transcript GRMZM2G025854_T02
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os10g11140.1 (Oryza sativa), 3'ss of exon 15
gtaccattgccatagagcttcactgttcattgtcatatatacaaactgacaaagtgttgtaaacctgtaatttctacttgatcatctaagactaagatgccacttcttagGTTCCAACAGGCTGGAAATTTTTTGGCAACCTAATGGATGCAGGAAAATTGTCTATTTGTGGAGAGGAAAGTTTTGGGACTGGATCTGATCACATCAGAG
||||  ||| ||  ||  | || ||| |||  |  | | | |||| |    ||      ||  ||  |   |||||   || || ||||||| |    | |||||   |||| |||||||| |||||||||||||| ||||||||||||||||| ||||||||||| ||||||||||||||||||||||| ||||||||||||||||| |
gtacttttgtcagtgaattgca-tgtgcatgatt-tgtttgcaaaatagtcaa------taggcc-atggcttctagaagaacagctaagacaatatggtcactttgcagGTACCAACAGGATGGAAATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGG

upper sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 15
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaccattgccatagagcttcactgttcattgtcatatatacaaactgacaaagtgttgtaaacctgtaatttctacttgatca--tctaagactaagatgcc---acttcttagGTTCCAACAGGCTGGAAATTTTTTGGCAACCTAATGGATGCAGGAAAATTGTCTATTTGTGGAGAGGAAAGTTTTGGGACTGGATCTGATCACATCAGAG
                  |||||  ||  | |||| | | |   | |  | | || ||| || |   |||  |      ||| |  | |  ||| |||   |    |  | ||||||||| || || |||||||||||||| || || |||||||| ||||||||||| || |||||||| || || ||||| || || |||||||||||| | |
-----------------gttcaccctttttagtca-acagatgtattttctaggt-ttgcaaccagataaaattaggaggataaactttttgacaaagcaacttgtatgttttagGTTCCCACTGGATGGAAATTTTTTGGAAATCTTATGGATGCTGGAAAATTGTCAATCTGTGGAGAAGAGAGCTTTGGCACAGGTTCTGATCACATCCGTG

upper sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 15
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 15
-------------gtacca--ttgccatagagcttcactgttcattgtcatatatacaaactgacaaagtgttgtaaacc--tgtaatttctacttgatcatctaagact---aagatgccacttctt------agGTTCCAACAGGCTGGAAATTTTTTGGCAACCTAATGGATGCAGGAAAATTGTCTATTTGTGGAGAGGAAAGTTTTGGGACTGGATCTGATCACATCAGAG
             |||| |  ||| | | ||    ||  |   | |||| |   || |||  || |   |  | |  |      || ||    | | |  | ||| | |    |  ||| |  |||||      |||| || || || |||||||||||||| ||||| |||||||| ||||| |||||||||||||| || ||||||||||| || || |||||||||||  | |
gtgaagcccttctgtactaatttgtcgt-gattaacatggaaaactgtcttgctta-aaatggaaaggtttatatccattgacatacttctctcctaacaaactatgtccttaacaatgactattcttggtttcagGTCCCCACTGGATGGAAATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTG

upper sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 15
lower sequence: EFJ34621 (Selaginella moellendorffii), 3'ss of exon 14
gtaccattgccatagagcttcactgttcattgtcatatatacaaactgacaaagtgttgtaaacctgtaatttc-tacttgatcatcta-agactaagatgccacttcttagGTTCCAACAGGCTGGAAATTTTTTGGCAACCTAATGGATGCAGGAAAATTGTCTATTTGTGGAGAGGAAAGTTTTGGGACTGGATCTGATCACATCAGAG
                                                     ||   | |  |     | ||  |     ||  |  | | |  || ||      |   |||||||||| |||||||| ||||||||||| || ||||| || |||||| |||| ||||| ||||||||||||||||| || ||||||||||| ||  | |
-----------------------------------------------------gtacgggacgctaccgactttatgagcaatggttcacacagcaaaat----tgttgaagGTTCCAACTGGCTGGAAGTTTTTTGGCAATCTCATGGACGCGGGAAAACTGTCGATTTGCGGAGAGGAAAGTTTTGGAACGGGATCTGATCATATTCGTG

upper sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 15
lower sequence: EFJ32824 (Selaginella moellendorffii), 3'ss of exon 14
gtaccattgccatagagcttcactgttcattgtcatatatacaaactgacaaagtgttgtaaacctgtaatttctacttgatcatctaagactaagatgccac--ttctt--agGTTCCAACAGGCTGGAAATTTTTTGGCAACCTAATGGATGCAGGAAAATTGTCTATTTGTGGAGAGGAAAGTTTTGGGACTGGATCTGATCACATCAGAG
                                                          |||         |  | |||| || | | | | || | |   ||   || ||  |||||||||| |||||||| ||||||||||| || ||||| || |||||| |||| ||||| ||||||||||||||||| || ||||||||||| ||  | |
----------------------------------------------------------gtacggg-acgctaccgactttatgagcgatggctcacacagcaaaattgttgaagGTTCCAACTGGCTGGAAGTTTTTTGGCAATCTCATGGACGCGGGAAAACTGTCGATTTGCGGAGAGGAAAGTTTTGGAACGGGATCTGATCATATTCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtaaacctgtaatttctacttgatcatctaagactaagatgccacttcttagGTTCCAACAGGCTGGAAATTTTTTGGCAACCTAATGGATGCAGGAAAATTGTCTATTTGTGGAGAGGAAAGTTTTGGGACTGGATCTGATCACATCAGAG
                    acttgat  putative branch site (score: 5)
                                            ccacttctt  putative PPT
            taatttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccattgccatagagcttcactgttcattgtcatatatacaaactgacaaagtgttgtaaacctgtaatttctacttgatcatctaagactaagatgccacttcttagGTTCCAACAGGCTGGAAATTTTTTGGCAACCTAATGGATGCAGGAAAATTGTCTATTTGTGGAGAGGAAAGTTTTGGGACTGGATCTGATCACATCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA