ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CAGAGGGCACAAAAATGAAAAGAACTTCGTTGGATTGTCTGTGAACAATGAGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTGTTTATCACAAGgtaatcgcaagcttctggcttggtcttgttcccgtgcagcatgcattgttacgatgtgtgattcaccttgatcagtaagatgtgttcctaacttcacactggttgcag

Basic information

species	Zea mays
transcript	GRMZM2G126795_T01
intron #	13
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 12

CAGAGGGCACAAAAATGAAAAGAACTTCGTTGGATTGTCTGTGAACAATGAGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTGTTTATCACAAGgtaatcgcaagcttctggcttggtcttgttcccgtg--cagcatgcattgttacgatgtgtgattcacctt---gatcagtaagatgtgttccta-acttcacactggttgcag---------------------
|||||||||||| |||||||||||||| |||||  ||||||| || || ||||| ||||| || || |||||||| ||||||||||||||||| ||||||||||| |||||||| | || || ||||||| ||||       || ||   ||| |     || || ||  |   | |  ||    ||||   | | |   ||  ||   | ||                      
CAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTGTTTACCACAAGgtaattgcaagcttattgcctgctcttgtttccgtatctgtgattcagcattatgtgccatgcttaactgtacaggttggtctcctgtggcaccatataccattctaacttcaagtaactctgtaccaattgcag

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA02G43540.1 (Glycine max), 5'ss of exon 12

CAGAGGGCACAAAAATGAAAAGAACTTCGTTGGATTGTCTGTGAACAATGAGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTGTTTATCACAAGgtaatcgcaagcttctggcttggtcttgttcccgtgcagcatgcattgttacgatgtgtgattcaccttgatcagtaagatgtgttcctaacttcacactggttgcag
|| ||| ||   |||||| || ||||| |||||  |  | || | || ||| |||||||| ||||| |||||||||||||| || |||||||| ||||||||  | |   | ||     |  || | |||  | ||  ||||  |   ||   || | || | |    |||  | | |  ||   | |    ||||            
CAAAGGCCATGCAAATGAGAAAAACTTTGTTGGTCTTACAGTAAGCAGTGAATATATTGCGTGTGGCAGTGAAACAAATGAAGTCTTTGTTTACCACAAGgt--ttgtg-gttttcaattatgtgtcgttttcttgt-gcatttaccttt--tatttatggtac----tgaggattcaagtgcccttcct-tttcag-----------

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 14
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 12

CAGAGGGCACAAAAATGAAAAGAACTTCGTTGGATTGTCTGTGAACAATGAGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTGTTTATCACAAGgtaatcgcaagct--tctggcttggtcttgttcccgtgcagcatgcattgttacgatgtgtg-attcaccttgatcagtaagatgtgttcctaacttcacactggttgcag
|||||| ||||  ||||| ||||||||||| ||  | ||||| |||| ||| |||||| ||||||| ||||||||||| || || || || || || ||||| |     | ||  |||        |   ||  | ||||   | |  |  ||| | |  |  |||       |    || ||   | |  ||   |              
CAGAGGACACACTAATGAGAAGAACTTCGTGGGCCTCTCTGTAAACAGTGAATATATTTCTTGTGGCAGTGAAACAAACGACGTCTTCGTCTACCATAAGgttagtagtacctgatcttaaaacagccaattttcatgcattttactattatactaagaatccatttgatagtaattctaggaaacgcttttactatttt-----------

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 14
lower sequence: PP1S264_64V6.1 (Physcomitrella patens), 5'ss of exon 13

CAGAGGGCACAAAAATGAAAAGAACTTCGTTGGATTGTCTGTGAACAATGAGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTGTTTATCACAAGgtaatcgcaagcttctggcttggtcttgttcccgtgcagcatgcattgttacgatgtgtgattcaccttgatcagtaagatg-tgttcctaacttcacactggttgcag
 ||||| || |  || |||||||| || |||||  | ||||| |||| ||| ||||| | |||||| |||| |||||||||||| |||||||| ||||||||||      | |||||  | |  || || | | |   |   |   ||  |   | |||  || ||       |||||  |  ||||  | || |    || ||     
GAGAGGACATACCAACGAAAAGAATTTTGTTGGGCTATCTGTTAACAGTGAATATATAGGTTGTGGTAGTGTAACAAATGAGGTGTTTGTTTACCACAAGgtaacgttttgtttctgtttagtactagtgcacattgtgatcg---tggaatcttttgttttttacaacttcaagtaaacttctgtttatgacctt-tgcttgt-----

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 14
lower sequence: PP1S37_28V6.1 (Physcomitrella patens), 5'ss of exon 12

CAGAGGGCACAAAAATGAAAAGAACTTCGTTGGATTGTCTGTGAACAATGAGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTGTTTATCACAAGgta-----atcg-caagcttctggcttggtcttgttcccgtgcagcatgcattgttacga--tgtgtgattcaccttgatcagtaagatgtgttcctaacttcacactggttgcag------------------------------------
  |||| ||||  ||||||||||| || || ||  |  |||| || | ||| || || |||||||| |||||||| |  ||||||||||| ||||||||||||     || |  ||| ||    | |  | | |  |  ||      | || | ||  ||  | | |  || |  ||||   |  |  || ||| ||   |||   | |  ||                                       
TGGAGGACACACCAATGAAAAGAATTTTGTGGGGCTTACTGTAAATAGTGACTACATCGCTTGTGGCAGTGAAACGAGCGAGGTTTTTGTATATCACAAGgtatggctatagataagattacatcctt-tgtagccctagtttgtttttcacttttctgaatttttttgttgatattgaagtgccacctgggttactcttttccttccgactgtgaatcactctcaccaagcgctttctgtttgtaccacag

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 14
lower sequence: PP1S154_52V6.1 (Physcomitrella patens), 5'ss of exon 12

CAGAGGGCACAAAAATGAAAAGAACTTCGTTGGATTGTCTGTGAACAATGAGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTGTTTATCACAAGgtaatcgcaagcttctggcttggtcttgttcccgtgcagcatgcattgttacgatgtgtgattcac-cttgatcagtaagatgtgttcctaacttcacactggttgcag
|||||| |||| |||||| ||||| || || |||||| |||| ||||||||||||||||| || || |||||| ||||||||||||| || ||||| ||||| |   | ||  |||  | |   ||| |||| |     ||   ||||| || |  |||| | ||   ||  |   |   |  | |  | || ||  || |        
CAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCGTGTATCATAAGgttagacccagactcta-catacactttttccagatt--cactgattgt-acaac-tgtggtgcagattttgtttttgcaacatttctccaatttaccagtctcc----

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 14
lower sequence: PP1S86_153V6.1 (Physcomitrella patens), 5'ss of exon 12

CAGAGGGCACAAAAATGAAAAGAACTTCGTTGGATTGTCTGTGAACAATGAGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTGTTTATCACAAGgtaatcgcaagcttctggcttggtcttgttcccgtgcagcatgcattgttacgatgtgtgattcaccttgatcagtaagatgtgttcctaacttcacactggttgcag
 | ||| ||||  ||||||||||| || |||||| |  |||| |||| ||||||||| || ||||| ||||||||||| ||||| ||||| |||||||||||||      ||||    |   || ||  |    ||   | |||  ||    ||||  |  |  || |||      || | |        |||| |      ||    
AAAAGGTCACACCAATGAAAAGAATTTTGTTGGACTTACTGTCAACAGTGAGTATATCGCCTGTGGCAGTGAAACAAACGAGGTGTTTGTGTATCACAAGgtaacattctgcttg-aacagagtgttaatattttgtgacttgctgtg----gatgactattggactttggatgtcaaaaggaaa---ggacttaaggtgaatttttt

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 14
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 5'ss of exon 12

CAGAGGGCACAAAAATGAAAAGAACTTCGTTGGATTGTCTGTGAACAATGAGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTGTTTATCACAAGgtaatcgcaagcttctggcttggtcttgttcccgtgcagcatgcattgttacgatgtgtgattcaccttgatcagtaagatgtgttcctaacttcacactggttgcag
 | ||| ||||  |||||||||||||| ||||||||| |||| ||||  || || || || ||||| |||||||| || ||||| ||||| ||||| |||||| |  |  | || |    || ||| |||    |  || ||  |   | ||| |  ||| ||        || ||    ||| | | | |    |       |    
GAAAGGACACACCAATGAAAAGAACTTTGTTGGATTGACTGTCAACAGCGAATACATCGCCTGTGGCAGTGAAACGAACGAGGTGTTTGTGTATCATAAGgtattgtcctgattgta---tgttctggttttaatttagaatttac-atgacgtttcgtgttttttagaactcggttt--tgtatacatgaggcaaagtgaaattt--

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 14
lower sequence: PP1S180_148V6.1 (Physcomitrella patens), 5'ss of exon 12

CAGAGGGCACAAAAATGAAAAGAACTTCGTTGGATTGTCTGTGAACAATGAGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTGTTTATCACAAGgtaat-cgcaagcttctggcttggtcttgttcccgtg----cagcatgcattgttacgatgtgtg---attcacc----------ttgatcagta-agatgtgttcctaacttcacactggttgcag--------------------------------------------------------
 ||||| || | ||| || ||||||||||| ||  || | || || || || ||||||||||| || |||||| ||||||||||| | || ||||| ||||||||  ||  ||||         |   ||| || ||     |||||   | || |  || |      ||| | |          ||  | || | | ||||    ||  || | || ||                                                               
TAGAGGACATACAAACGAGAAGAACTTCGTGGGGCTGACCGTCAATAACGAATATATTGCTTGCGGCAGTGAATCAAATGAGGTTGTCGTGTATCATAAGgtaatatgctggctttacttacacttcagttgccttgattgtagcatctttggtcagaatatccatcaatttatcaacctgcttttttttgagcatacatgtacctctttctgcgcattgaacctgctctctttcattattaggtttcacgattctgagaccgttttttttgcattttggcag

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|149104054|gb|EE289486.2|EE289486

EST:     AGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTGTTTATCACAAG                         GCTATCTCAAAACCAGCAGCAAGCCATAGATTTGTATCCTCTAACCTGGAT
genomic: AGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTGTTTATCACAAGgtaatcgcaa ... ctggttgcagGCTATCTCAAAACCAGCAGCAAGCCATAGATTTGTATCCTCTAACCTGGAT

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