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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgtcatcagttgactctgccccctgtgttcttttcctcaacgttaacagcatttgtgtttttgagcagGAAGTTCCAGACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA

Basic information

species Zea mays
transcript GRMZM2G013115_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128748_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g50750.3 (Oryza sativa), 3'ss of exon 10
------------------------------------------------------------------------gtaa-gtcgtcatcagttgactctgccccctgt---gttcttttcctcaacgttaacagcatttgtgtttttgagcagGAAGTTCCAGACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
                                                                        |||| |     ||  |||   | || ||  ||    ||        | |||  |  | |  ||  | ||  ||| |||||| ||||||| || |||||||| ||||| ||||| |||||||| || || || ||||||||||||||||| || |||||||| ||||||||||| || |
gtaagtttagtattcagtatttcagttccttgtgccctttgttctacgaattcatagcttgctaccaagactgtaaagctactatttgttctttgtgaccattgcaaagtctaaagttttaaccctgtctg--ttcttcttactgaacagGAAATTCCAGATAACGAGTTTGAGAAGCGCATCAGGCCAGAGGTTATACCAGCCAGTGAGATAGGAGTGACTTTTGATGACATTGGAGCCCTGGCTGACA

upper sequence: GRMZM2G128748_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 10
---------------------------gtaagtcgtcatcagttgactctgccccctgtgttcttttcctcaacgtta-acagcatttgtgtttttgagcagGAAGTTCCAGACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
                            ||| |  | | |   |  |  |   |  ||    |||||         || | |  | |||  |  ||  |||||||||||| ||||| |||||||| ||||| || ||||||||||| || || |||| ||||||||| || ||||| |  || || || ||  |||  || |
ctagccatgtaactgaagctgtgtgatataaattctaaacttatttccttttactttgcccccttttttgtgttactatatactaattgcttgctt--gcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCGTTGGATGAGA

upper sequence: GRMZM2G128748_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA16G29040.1 (Glycine max), 3'ss of exon 10
---------------------gtaagtcgtcatcagttgactctgccccctgtgttcttttcctca---acgttaacagcatttgtgtttttga--gcagGAAGTTCCAGACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
                     ||| |   | |    |  |||     || | |  | |   |||       ||||  |     |   || |||   |||||||||||| ||||| |||||||| ||||| || ||||||||||| || || |||| ||||||||| || ||||| |  || || || ||  |||  || |
actagccatgcagctgaagctgtatgatttaaattctaaacttatttccttttactttcccccttttttgtgttactatatactaatttcttgcttgcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCATTGGATGAGA

upper sequence: GRMZM2G128748_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv02s0025g00650.t01 (Vitis vinifera), 3'ss of exon 11
-------------------gtaagtcgtcatcagttgactctgccccctgtgttcttttc-----ctcaacgttaacagcatt--tgtgtttttg-agcagGAAGTTCCA---GACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
                    |||   ||  ||| | |  | ||       |    ||||       | |||||| | ||   |  | | ||||   | |||||||||||    |||||||| ||||| ||||| ||||||||||||||||| || || |||||||| || |||||||| | ||| || || ||| |||  |   
tttgtttaatttacaaaaaataatctgtt-tcaatcgcatttgattttcttaccttttttgtagttttaacgttgaaaggcctgctatattttcctaacagGAAGTTCCTCCTGACAATGAATTTGAGAAGCGCATCAGACCAGAGGTCATCCCAGCTAGTGAGATTGGTGTGACATTTGCTGATATTGGTGCCATGGATG---

upper sequence: GRMZM2G128748_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 12
-------------------------gtaagtcgtcatcagttgactctgccccctgtgttcttttcctcaacgttaacagcatttgt-gtttttgagcagGAAGTTCCA---GACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
                         | || |  |  |  |   | | | |  | |    |   |   | |||  |   |   ||  | ||||     ||||||||||||   |||||||| ||||| |||||||| || |||||||| || || || | |||||||||||||||||| ||||| ||||| ||  ||   |   
gatcacaatgctgatttttgtaaaagaaaattttattgggaaaattttccatcattcccttactcttttaactgttgaactgttaattgtttccctccagGAAGTTCCACCTGACAATGAATTTGAGAAGCGTATAAGGCCAGAGGTTATCCCAGCGAATGAGATAGGAGTGACATTTGATGATATCGGTGCTTTGAGTG---


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgccccctgtgttcttttcctcaacgttaacagcatttgtgtttttgagcagGAAGTTCCAGACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
                           cgttaac  putative branch site (score: 3)
                                          tgttttt  putative PPT
              ttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcgtcatcagttgactctgccccctgtgttcttttcctcaacgttaacagcatttgtgtttttgagcagGAAGTTCCAGACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT