Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctcaacttgaagaaaaaatcgtgcttttctagtctatagttaaaagatttcagtgtagacttgtaaacgtgtcgattgtcacag

Basic information

species Zea mays
transcript GRMZM2G092517_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092517_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g60960.1 (Oryza sativa), 5'ss of exon 2
GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctcaacttgaagaaaaaatcgtgcttt---tctagtctatagttaaaagatttcagtgtagacttgtaaacgtgtcgattgtcacag
||| |||||||||||||| |||||||||||||| ||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||| |||||      ||  ||  ||   ||| | | | ||   |     || | | ||     |       | |  | ||    |    |   ||  |||
GGAGTGCCCCTTCGCCCCCTACTTCTCGCCGCACGAGCCCCACAAGTTCGCCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgatacca--ttacaggtcaaagcattccttaaattgtacctttcgctagcttgtgcattaatggcttcgtcggtgcaatg-cggtttcag

upper sequence: GRMZM2G092517_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA04G39830.1 (Glycine max), 5'ss of exon 1
GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctca-------acttgaagaaaaaatcgtgcttttctagtctatagttaaaagatttcagtgtagacttgtaaacgtgtcgattgtcacag--------------------
 ||||| |||||  | || || ||||| || ||||||||||| ||||| ||  | |||||||| || || || || ||||||||||| ||||||||| |||||||  | ||       |||  |   | ||||    ||       |   ||  |||   ||   |   || || |||     |  |  || | | ||                    
AGAATGTCCCTTTTCTCCATATTTCTCTCCCCATGAGCCCCAAAAATTTGCTTCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCAAAGATGCTCATGgtaaatacacacacacacactgtacacataaataacactggctagctagttatctaattaatcatatcatatacatgt--gtattccacttattatagatttcaatcatatgttgtag

upper sequence: GRMZM2G092517_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA06G15050.1 (Glycine max), 5'ss of exon 1
GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctcaacttgaagaaaaaatcgtgcttttctagtcta-tagttaaaagattt-cagtgtagacttgtaaacgtgtcgattgtcacag------------------------------------------
 ||||| |||||  | || || ||||| || |||||||| || || || ||  | |||||||| ||||| || || ||||||||||| ||||||||| |||||||    ||     | |  | |           ||||     ||||||    |||  |  | |    |   |    |  |  || | | ||                                          
AGAATGTCCCTTTTCTCCATATTTCTCTCCCCATGAGCCTCAAAAGTTTGCTTCTGTCCACAAAGTCTTTGGTGCCAGCAACGTCTCAAAGATGCTCATGgtaaatatacacacacacggtacacataaataacactagctagctagttatttaattaaccatatcatataacatgtattccacttattatagattttaatcatatcatataatttcttcgacaatgtgttgtag

upper sequence: GRMZM2G092517_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT2G30340.1 (Arabidopsis thaliana), 5'ss of exon 2
GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaag----cctcaacttgaagaaaaaatcgtg--cttttctagtctatagttaaaagatttcagtgtagacttgtaaacgtgtc-gattgtcacag--
||| || || ||| | |||||||||||||||||||| || ||||| ||||| ||||| || || ||||| || || ||||||||||||||||||||  ||||| |       || || | ||  || | |  |   |||||||    ||  |||     |||| | |      |||  | ||| |  ||||         
GGAGTGTCCTTTCTCGCCTTACTTCTCGCCGCATGAACCTCACAAGTTCGCTGCCGTTCATAAAGTCTTTGGTGCAAGCAACGTCTCCAAGATGCTTCTGgtacacatattttctacattaatgaatatttattttcttttcttagttaaggtttcttaatttgattactcttttgatatcgtatttgattaatctgaat

upper sequence: GRMZM2G092517_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT2G40470.1 (Arabidopsis thaliana), 5'ss of exon 2
GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaa-agcc---tcaa----cttgaagaaaaaatcgtgcttttctagtctatagttaaa-agatttcagtgtagacttgtaaacgtgtcgattgtcacag
 ||||| |||||  | || || ||||| || || ||||| || || |||||  |||||||||| ||||| || ||||| |||||||||||||||||  |||||| ||||   ||||    |    ||| |   || || |||     |  ||  ||| | |  |  || |    |  ||            | |||| | 
AGAATGTCCCTTTTCGCCATATTTCTCCCCACACGAGCCTCATAAGTTCGCTTCCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGCTAATGgtaatagccatttcaaaacacacatagatatggtcttgatttatgcatgcattattacatatgtaacaataaccaactgatggtaatctagtggtcatat

upper sequence: GRMZM2G092517_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv06s0004g07790.t01 (Vitis vinifera), 5'ss of exon 2
GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctcaacttgaagaaaaaatcgtgcttttc----tagtctatagttaaaagatttcagtgtagacttgtaaacgtgt-cgattgtcacag
 || ||||| ||| |||| || ||||| || ||||| || ||||| || || || |||||||| || || || || ||||||||||||||||||||| |||||||||| ||  |   |   ||  |     | |||       ||||   ||   |  |||   | || | || ||  | | | | |||       
AGAGTGCCCTTTCTCCCCCTATTTCTCCCCCCATGAACCTCACAAGTTTGCTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaaagccccagttcccatctaatcttacagtcttcataacgttctacccttctgatgttttcttctataatt-tatgcatatacaattag-----

upper sequence: GRMZM2G092517_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv13s0067g02380.t01 (Vitis vinifera), 5'ss of exon 2
GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctcaacttgaagaaaaaatcgtgcttttctagtctatagttaaaagatttcagtgtagacttgtaaacgtgtcgattgtcacag
 |||||||||||  | || |||||||| || ||||| ||||| || || ||  |||| ||||| ||||||||||| ||||||||||||||||||||| ||||| | ||  || |      |  | | ||   ||||  ||   |  || |  |||  |     | |  | || || |||  | | |||   
AGAATGCCCCTTTTCTCCCTACTTCTCTCCCCATGAACCCCAGAAGTTTGCTTCCGTTCACAAAGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCATGgtagaaccctaattctgtctaccagtagta--tttcatgttcttgattgattgataacttctcaaatct-tacac-tgttaaat-tcag--

upper sequence: GRMZM2G092517_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ35900 (Selaginella moellendorffii), 5'ss of exon 1
GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctcaacttgaagaaaaaatcgtgcttttctagtctatagttaaaagatttcagtgtagacttgtaaacgtgtcgattgtcacag-------------
 || || ||||| || || ||||||||||| || ||||| || || || |||||||||||||| || |||||||| |||||||||||||||||||||| ||||     |||| |           || | |  |   | ||   ||    |  ||| || |||    || |||  |   |  || || |               
AGAGTGTCCCTTTGCACCATACTTCTCGCCACACGAGCCTCAAAAGTTTGCCGCCGTCCACAAAGTTTTCGGCGCCAGCAACGTCTCCAAGATGCTCTCGgtacgtgatcaa-tcatccctcttctcttcccgtggcaatccg-agcaccactattccattgtc--tttctaagtggtactcttttctctttcggagtgtgctt

upper sequence: GRMZM2G092517_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ09483 (Selaginella moellendorffii), 5'ss of exon 1
GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctcaacttgaagaaaaaatcgtgcttttctagtctat---agttaaaagatttcagtgtagacttgtaaacgtgtcgattgtcacag--------
 || || ||||| || || ||||||||||| || ||||| || || || |||||||||||||| || |||||||| |||||||||||||||||||||| ||||     ||||              |   |||  |  | |  |   ||    |  ||| || |||    || |||  |   |  || || |          
AGAGTGTCCCTTTGCACCATACTTCTCGCCACACGAGCCTCAAAAGTTTGCCGCCGTCCACAAAGTTTTCGGCGCCAGCAACGTCTCCAAGATGCTCTCGgtacgtgatcaatcatctctcccctcctctcttcccgtggccctccgagcaccactattccattgtc--tttctaagtggcactcttttctctttcggagtg

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|101393630|gb|EB818747.1|EB818747
EST:     CCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTG                         GAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAA
genomic: CCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctc ... attgtcacagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAA
EST: gi|101393628|gb|EB818746.1|EB818746
EST:     AGCAACGTCTCCAAGATGTTCTTG                         GAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAA
genomic: AGCAACGTCTCCAAGATGCTCTTGgtaaagcctc ... attgtcacagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAA
EST: gi|211271838|gb|FK962424.1|FK962424
EST:     CCGCCGTCCACAAGGTCTTCGGCGCTASSAACGTCTCCAAGATGCTCTTG                         GAGGTGGTGGAGGGGGAGA
genomic: CCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctc ... attgtcacagGAGGTGGTGGAGGGGGAGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 3 RNA-Seq libraries.


Block sizes: 23 (upstream exon), 31 (downstream exon)
Score: 2

GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctc ... attgtcacagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAAGCGAACCTCCGGTTGCGGGATCCGGTGTACGGATGCATGGGCGCCATCT


Block sizes: 31 (upstream exon), 29 (downstream exon)
Score: 5

GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctc ... attgtcacagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAAGCGAACCTCCGGTTGCGGGATCCGGTGTACGGATGCATGGGCGCCATCT


Block sizes: 38 (upstream exon), 35 (downstream exon)
Score: 6

GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctc ... attgtcacagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAAGCGAACCTCCGGTTGCGGGATCCGGTGTACGGATGCATGGGCGCCATCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctcaacttgaagaaaaaatcgtgcttttctagtctatagttaaaagatttcagtgtagacttgtaaacgtgtcgattgtcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG