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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTACAGTCATTGCAACGACAAGTGGAGgtagtgatagtgcatctgtagttgaattgctttggaatatgtgtgacatcttgttagtatatataatccagttctaatacaatttcgaacttgcag

Basic information

species Zea mays
transcript GRMZM2G092091_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092091_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g51910.1 (Oryza sativa), 5'ss of exon 5
ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTACAGTCATTGCAACGACAAGTGGAGgtagtgatagtgcatctgtagttgaattgctt-tggaatatgtgtgacatcttgttagtatatataatccagttctaatacaatttcgaacttgcag
|||||||| |||||||||||||| |||||||| ||||| |||||||||||| | ||||| ||||| |||||| |  ||| |     || ||| | ||  || | | | |  ||  | |||         | | |||||      ||| ||||| | ||||||||||
ATCACTGGTAAGGCAGTCATGCTTGATGAGATAATCAATTATGTACAGTCACTACAACGTCAAGTTGAGgtactattagggtg---gtggttcagttatttcttggacagttggaatatcac-------tctgtaatc------taacacaatct-gaacttgcag

upper sequence: GRMZM2G092091_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT1G10120.1 (Arabidopsis thaliana), 5'ss of exon 4
ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTACAGTCATTGCAACGACAAGTGGAGgtagtgatagtgcatctgtagttgaattgctttggaatatgtgtgacatcttgttagtatatataatccagttct---aatacaatttcgaacttg--cag
||||| || || || || ||||||||||| || ||||||||||| |||||||||||||  ||||| ||||||   | | |    | ||| |   |     ||| ||       |  |  ||| |   | | |   |    ||||   || ||   ||  |  ||   |||
ATCACCGGAAAAGCGGTTATGCTCGATGAAATAATCAACTATGTTCAGTCATTGCAACAGCAAGTTGAGgta---agattatcccagtaatgcgagattcttgaaactctcaagttagtttggtgtgaaagaggttttctttcttgaaaaactgcttttattttcttcag

upper sequence: GRMZM2G092091_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv18s0001g08600.t01 (Vitis vinifera), 5'ss of exon 4
ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTACAGTCATTGCAACGACAAGTGGAGgta-gtgatagtgcatctgtagttgaattgctttggaatatgtgtgacatcttgttagtatatataatccagttctaatacaatttcgaacttgcag-----------
|| ||||| |||||||| ||||| |||||||||||||| |||||||||||| |||||| ||| || |||||| |  || || || || || |  |        ||   ||  |||   |  || |  | | ||  ||  |  | ||| | ||  |    ||                
ATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCACTGCAACAACAGGTTGAGgtatgccattgttcaactctaatata--------ggggcattagtggtgttgtgctgttgtttaagatttatatttaagaaaaagttagcctcatcaatccttatatg

upper sequence: GRMZM2G092091_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv07s0151g00450.t01 (Vitis vinifera), 5'ss of exon 4
ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTACAGTCATTGCAACGACAAGTGGAGgta-gtgatagtg-catctgtag------ttgaattgctttggaatatgtgtgacatcttgttagtatatataatccagttctaatacaatttcgaacttgcag
|| ||||| || || || ||||| |||||||||||||||||||| || ||| |||||||||| || |||||| | | |  ||  ||||| ||      ||  ||  ||||   ||   | | | |||   | |  |  |    | | |   |   |  || |  ||||     
ATTACTGGAAAAGCGGTAATGCTTGATGAGATTATCAACTATGTGCAATCACTGCAACGACAGGTTGAGgtatgcgtttctgatatctgaagaataagtttcatctctttattatgaatataaaatcacatgaagaattcctctgctgacttttaaagatctgaaacta----

upper sequence: GRMZM2G092091_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S68_190V6.1 (Physcomitrella patens), 5'ss of exon 3
-------------------------------ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTACAGTCATTGCAACGACAAGTGGAGgtagtgatagtgc--atctgtagttgaat-----tgctttggaatatgtgt----gacatc-ttgttagtatatataat--ccagttctaatacaatttcgaacttgcag--------------------------
                                |||| ||||||||||||||||| || ||||| ||||||||||| || ||  | ||||||||||| || |||    |  | |  || |  |    | |     |||| |   ||   |||    | || | || ||  |||   || |    | || || |  | | | ||  ||| |                           
CCTGCAGGACCTCGTACCCGGCTGCCGCAAAGTCACCGGCAAGGCAGTCATGCTTGACGAGATCATCAACTATGTTCAATCCCTCCAACGACAAGTTGAAgtatgtctcttacccattttcaacgcactgctaatgctattccattcatgtcttaggcacccttcttgttatcgctagtgatgaattgtagtctagtattgag-ttgtatcgtacactttgttatcttttttacag

upper sequence: GRMZM2G092091_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S69_95V6.1 (Physcomitrella patens), 5'ss of exon 2
-------------------------------ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTACAGTCATTGCAACGACAAGTGGAGgtag-------------tgatagtgcatctgtagttgaat-tgct--ttggaatatgtgtgacatcttgttagtatatataatccagttctaatacaatttcgaacttgcag
                                |||||||||| ||||||||||||||||| || ||||| || || |||||  | ||||| ||||| ||||||               |    |  ||    | |||||  || |  | || || ||    |  || | | ||  |||    |  | ||| |  |   |||     ||||||
CTTGCAGGACCTTGTTCCTGGCTGCCGCAAAGTCACTGGCAAAGCAGTCATGCTCGATGAAATCATCAATTACGTCCAGTCCCTCCAACGTCAAGTCGAGgtacatccctcattctccgccgttctatacacaattgaaggtggtgatagggatctgctgtaattcatatcaggttatgatgttaacttcca-cattttttttgtgttgcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|71759634|gb|DR957571.1|DR957571
EST:     GACAAGGGGAG                         TTCTTGTCAATGAAACTTTCAACTGTTAACCCTGAACTTGGCTTTGACATG
genomic: GACAAGTGGAGgtagtgatag ... gaacttgcagTTCTTGTCAATGAAACTTTCAACTGTTAACCCTGAACTTGGCTTTGACATT
EST: gi|211393687|gb|FL093754.1|FL093754
EST:     TGCTCGATGAGATTATCAACTATGTACAGTCATTGCAACGACAAGTGGAG                         TTCTTGTCAATGAAACTTTCAACTGTTAACCCTGAACTTGGCTTTG
genomic: TGCTCGATGAGATTATCAACTATGTACAGTCATTGCAACGACAAGTGGAGgtagtgatag ... gaacttgcagTTCTTGTCAATGAAACTTTCAACTGTTAACCCTGAACTTGGCTTTG
EST: gi|211393688|gb|FL093755.1|FL093755
EST:     TGCTCGATGAGATTATCAACTATGTACAGTCATTGCAACGACAAGTGGAG                         TTCTTGTCAATGAAACTTTCAACTGTTAACCCTGAACTTGGCTTTGACATT
genomic: TGCTCGATGAGATTATCAACTATGTACAGTCATTGCAACGACAAGTGGAGgtagtgatag ... gaacttgcagTTCTTGTCAATGAAACTTTCAACTGTTAACCCTGAACTTGGCTTTGACATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTACAGTCATTGCAACGACAAGTGGAGgtagtgatagtgcatctgtagttgaattgctttggaatatgtgtgacatcttgttagtatatataatccagttctaatacaatttcgaacttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG