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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaccctttagcatggaacattatcatactgcagtacaatgctggttgctggtctttttattaatctgtatgttattgcaatgatagGTCCGACTTATGCTGGTCCTTGCTCCTGCTGCATGCATTTTGTCTGGGATTGCTCTGTCTGAAGCTTTTGGTGTCCTTACAAGATCAATGAAATTTCAGC

Basic information

species Zea mays
transcript GRMZM2G154165_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA16G08410.1 (Glycine max), 3'ss of exon 14
gtaaaaccctttagcatggaacattatcatactgcagtacaatgctggttgctggtctttttattaatctgtatgttattgc--aatgatagGTCCGACTTATGCTGGTCCTTGCTCCTGCTGCATGCATTTTGTCTGGGATTGCTCTGTCTGAAGCTTTTGGTGTCCTTACAAGATCAATGAAATTTCAGC
             | | | |  || ||     |       | |  ||  |  |  |  ||||||| |     ||  | ||||  |||   |||| ||  | ||||| || |||||||| |||||||| |||||||||||||||||||| ||| | ||||||| |||  | |||||||| || || || ||| 
-------------gtaagaataataatggagttttttcttactattgcatttttattattttattgagg-acataatcttgctgaatatcagGTTCGCTTGATGCTCGTACTTGCTCCAGCTGCATGTATTTTGTCTGGGATTGCTCTTTCTCAGGCTTTTGATGTTTTCACAAGATCTATTAAGTTGCAGT

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 14
gtaaaaccctttagcatggaacattatcatactgcagtacaatgctggttgctggtctttttattaatctgtatgttattgcaatgatagGTCCGACTTATGCTGGTCCTTGCTCCTGCTGCATGCATTTTGTCTGGGATTGCTCTGTCTGAAGCTTTTGGTGTCCTTACAAGATCAATGAAATTTCAGC
|||| |    | |    |||   || || ||||   | |         ||  |  | || ||    |  |  ||  |  || |||   |||| ||  | ||||| || |||||||| || ||||| || ||||||||||||||||| ||| | ||||||| |||  | |||||||| || || || ||| 
gtaagaataataatggaggaggtttttcttactattgcat-------ttttattattttattgaggacata-atcctgctg-aatatcagGTTCGCTTGATGCTTGTACTTGCTCCAGCAGCATGTATCTTGTCTGGGATTGCTCTTTCTCAGGCTTTTGATGTTTTCACAAGATCTATTAAGTTGCAGT

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 12
lower sequence: AT5G19690.1 (Arabidopsis thaliana), 3'ss of exon 14
gtaaaaccctttagcatggaacattatcata-----ctgcagtacaatgctggttgctggtctttttattaatctgtatgttattgcaatgatagGTCCGACTTATGCTGGTCCTTGCTCCTGCTGCATGCATTTTGTCTGGGATTGCTCTGTCTGAAGCTTTTGGTGTCCTTACAAGATCAATGAAATTTCAGC
||||      |    ||| |      |   |     |||  |   | |  |  ||  ||  |  | |||| | |||| |  |  ||   |  ||||| || |||||||| || |||||||| || ||||||||  ||||||||||||| || ||| ||||||||| |||  | ||  | || || ||||  ||| 
gtaagttgtgtgtctatgaattgccgttgcatctttctgttgcctagttatt-ttattgaaccatgtattcacctgtct--tcctgttctcttagGTTCGTCTTATGCTCGTGCTTGCTCCAGCAGCATGCATCATGTCTGGGATTGCGCTCTCTCAAGCTTTTGATGTTTTCACGGGTTCCATCAAATACCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtacaatgctggttgctggtctttttattaatctgtatgttattgcaatgatagGTCCGACTTATGCTGGTCCTTGCTCCTGCTGCATGCATTTTGTCTGGGATTGCTCTGTCTGAAGCTTTTGGTGTCCTTACAAGATCAATGAAATTTCAGC
                          tattaat  putative branch site (score: 2)
                      tttttattaatctgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaccctttagcatggaacattatcatactgcagtacaatgctggttgctggtctttttattaatctgtatgttattgcaatgatagGTCCGACTTATGCTGGTCCTTGCTCCTGCTGCATGCATTTTGTCTGGGATTGCTCTGTCTGAAGCTTTTGGTGTCCTTACAAGATCAATGAAATTTCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA