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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGGAGCATCTATTGGAGCAATTGGAGCTCAAAGTATTGGGGAGCCAGGGACTCAGATGACACTGAAAACATTTCATTTTGCGGGAGTAGCTAGCATGAgtatcctttttaccgctgcttcaggaaaatattactgaattctgtggcatttaaacatgctcaattaagatgcttcattttgtttttcagtttctttttc...

Basic information

species Zea mays
transcript GRMZM2G178236_T02
intron # 1
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178236_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g41490.1 (Oryza sativa), 5'ss of exon 20
GCAGGAGCATCTATTGGAGCAATTGGAGCTCAAAGTATTGGGGAGCCAGGGACTCAGATGACACTGAAAACATTTCATTTTGCGGGAGTAGCTAGCATGAgtatcctttttaccgc-tgcttcaggaaaatat-tactgaattctgtggcatttaaacatgctcaattaagatgcttcattttgtttttcagtttctttttc
|| |||||||| ||||| |||||||| |||||||||||||| ||||| || |||||||||||| ||||||| || |||||||| ||||||||||||||||||||||| | |||    || |||  |||| | |    | |||| |  |   |   | || |     ||    |  ||| | |  ||| |    ||       
GCCGGAGCATCAATTGGGGCAATTGGGGCTCAAAGTATTGGAGAGCCTGGAACTCAGATGACATTGAAAACTTTCCATTTTGCAGGAGTAGCTAGCATGAgtatcctatatactatatggttcgtgaaagtctgcttttaattttaagaattactagcaggtcgttttggcctatttcctataatttatttactttagag--

upper sequence: GRMZM2G178236_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA11G15530.1 (Glycine max), 5'ss of exon 18
GCAGGAGCATCTATTGGAGCAATTGGAGCTCAAAGTATTGGGGAGCCAGGGACTCAGATGACACTGAAAACATTTCATTTTGCGGGAGTAGCTAGCATGAgtatcctttttaccgctgcttcaggaaaat-attactgaattctgtggcatttaaacatgctcaattaagatgcttcattttgtttttcagtttctttttc
|| |||||  || |||| |||| ||||||||| |||||||| ||||| ||||| ||||||||  ||||||| || || ||||| ||||| || |||||||||||||||| |    |    |     |  |   || | | |   | |||||||      |   || |     | |||  |  |  | | || ||     ||
GCTGGAGCTCCTGTTGGTGCAACTGGAGCTCATAGTATTGGAGAGCCTGGGACCCAGATGACTTTGAAAACTTTCCACTTTGCTGGAGTTGCAAGCATGAgtatcctttatttgaccatgttgtctactttgataatcactaagggggcatttggtgggggataaatttttagtttc-ctgggaatgttagattggaaatc

upper sequence: GRMZM2G178236_T02 (Zea mays), 5'ss of exon 1
lower sequence: AT5G60040.1 (Arabidopsis thaliana), 5'ss of exon 21
GCAGGAGCATCTATTGGAGCAATTGGAGCTCAAAGTATTGGGGAGCCAGGGACTCAGATGACACTGAAAACATTTCATTTTGCGGGAGTAGCTAGCATGAgtatcctttttaccgctgctt--caggaaaatattactg-aattctgtggcatttaaacatgctcaattaagatgcttcattttgtttttcagtttctttttc--
|| ||  |  | |||||  |||| |||||||| |||||||| || || ||||| || |||||  ||||||| ||||| ||||| ||||| || ||||||||||||||| ||     ||| |        ||| |  ||  ||  ||   || | || | |||   | ||        |  ||||| ||| | | ||||  |||  
GCTGGGACTGCAATTGGGACAATAGGAGCTCAGAGTATTGGAGAACCTGGGACACAAATGACTTTGAAAACTTTTCACTTTGCTGGAGTTGCGAGCATGAgtatccttgttgaaaatgcctattttctgaatttcgctataaaactagtgcttatacatatgagtagttgg------ttgttttgatttcctgattctggttcag

upper sequence: GRMZM2G178236_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv06s0004g03730.t01 (Vitis vinifera), 5'ss of exon 1
GCAGGAGCATCTATTGGAGCAATTGGAGCTCAAAGTATTGGGGAGCCAGGGACTCAGATGACACTGAAAACATTTCATTTTGCGGGAGTAGCTAGCATGAgtatcctttttaccgctgcttcaggaaaatattactgaattctgtggcatttaaacatgctcaat----taagatgcttcattttgtttttcagtttctttttc--------------
|| ||| |  | ||||| |||||||||||||| |||||||| ||||| ||||| ||||||||| | ||||| || || ||||| || || || ||||||||||||||||| |||  ||    ||     |   ||    |||   ||   ||     |  | | |    |    |  ||  || || |   || | |  |  |               
GCTGGAACTGCAATTGGTGCAATTGGAGCTCATAGTATTGGAGAGCCTGGGACACAGATGACATTAAAAACTTTCCACTTTGCTGGTGTTGCAAGCATGAgtatccttttaaccattga--aagactcttggcacctttttccccggggcttttgtctattgagtcttctgtattttttttttctggtcaccaatgtggtactttaactctgtattag

upper sequence: GRMZM2G178236_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ13293 (Selaginella moellendorffii), 5'ss of exon 20
GCAGGAGCATCTATTGGAGCAATTGGAGCTCAAAGTATTGGGGAGCCAGGGACTCAGATGACACTGAAAACATTTCATTTTGCGGGAGTAGCTAGCATGAgta--tcctttttaccgctgcttcaggaaaatattactgaattctgtggcatttaaacatgctcaattaagatgcttcattttgtttttcagtttctttttc
 | ||| |  || ||||||| |||||||||||||||||||| || || || || ||||||||  ||||||| ||||| ||||| ||||| |||||||||||||  ||  | |    | |   ||         || || | | |  | || || |||                                             
CCTGGAACTGCTGTTGGAGCCATTGGAGCTCAAAGTATTGGAGAACCTGGAACGCAGATGACCTTGAAAACTTTTCACTTTGCTGGAGTGGCTAGCATGAgtaagtctctctcgttgttctctcg------cctttctaactgcctttgctttcaaag--------------------------------------------

upper sequence: GRMZM2G178236_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ24638 (Selaginella moellendorffii), 5'ss of exon 20
GCAGGAGCATCTATTGGAGCAATTGGAGCTCAAAGTATTGGGGAGCCAGGGACTCAGATGACACTGAAAACATTTCATTTTGCGGGAGTAGCTAGCATGAgtatcctttttaccgctgcttcaggaaaatattactgaattctgtggcatttaaacatgctcaattaagatgcttcattttgtttttcagtttctttttc
 | ||| |  || ||||||| |||||||||||||||||||| || || || || ||||||||  ||||||| ||||| ||||| ||||| |||||||||||||   | | |  || || |           || || | | |  | || || |||                                             
CCTGGAACTGCTGTTGGAGCCATTGGAGCTCAAAGTATTGGAGAACCTGGAACGCAGATGACCTTGAAAACTTTTCACTTTGCTGGAGTGGCTAGCATGAgtaag-tctctctcgttgttctctt---gcctttctaactgcctttgctttcaaag--------------------------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGGAGCATCTATTGGAGCAATTGGAGCTCAAAGTATTGGGGAGCCAGGGACTCAGATGACACTGAAAACATTTCATTTTGCGGGAGTAGCTAGCATGAgtatcctttttaccgctgcttcaggaaaatattactgaattctgtggcatttaaacatgctcaattaagatgcttcattttgtttttcagtttctttttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG