ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagtacataaacttcattgtttatgttctatccttcttctgtaatgatacttatacttgattgcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG

Basic information

species	Glycine max
transcript	GLYMA15G07330.1
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5

--gtaagtacataaacttcattgtttatgttctatcctt-cttctgtaatgatac----------ttata--cttgattgcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG
   | | | |||| |||| | || |  |||   |   || | | | | |  |||           |||||  |    ||| ||| |||||||| |||||||| |||||| | || ||||| || |||||| ||||||||||||| ||||||||| | |||||||| | ||||||   |   ||
gtatgattccatatactttactgatcttgtgtaactgttacatgtcttaacatatagatcttaaattataatccctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG

upper sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 5

---------------gtaagtacataaacttcattgttt-atg-ttctatccttcttctgtaatgatacttatacttga--ttgcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG
               || | |   | |     | || |  ||| ||  |   ||  ||  |||  ||| || || |  |  ||||||| ||||| |||||||| ||||||||| | || ||||| || |||||| | || |||||||||||||||||| | || ||||| | | |||||  |   ||
gtatgtttgcaatgagttattgttttactcatactgctagatgatttgaatgttactcgttaaccatatttctattgtatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG

upper sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5

gtaagtacat--aaacttcattgtttatgttctatccttctt-----ctgtaatga-tacttatacttgatt---gcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG
|||||| |    || |  |  || |    | | || |||| |      | || | | |  ||  | || |||     ||| || |||||||||||||||||||| ||||| ||||||||||||||  | || ||||| || |||||||| || || || || || || || ||||| ||
gtaagtcctctgaagcaaccatgatatgatacgattcttcatgatatttctattaactgtttgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG

upper sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 5

-------------------------gtaagtacataaacttca--ttgtttatgttct---atccttcttctgtaatgatacttatacttgatt--gcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG
                          | | || || ||    |  ||   | | || |   |   | | ||   ||  || || ||  |  |||    ||| |||||||||||||||||||||||  |||| ||||| || |||||| | || |||||||||||||||||  | || ||||| | | |||||      ||
gtatgtgtgacacactgttgatttactcattagatgaaacaaagattacctgtatttttagaatttgcatcgccaagcatgctgattttgtatttattagTGTACAAGAAGCACTACCCACCTGCGCTGAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGCGCATTCCACAAGAAGTTAAATGCCAGTGG

upper sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6

------------------------------------------gtaagtacataaacttcattgtttatgttctatccttcttctgtaa-tgatacttatacttgattgcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG
                                           ||  | ||||||  |   | | | | |   ||  |  |  || |  ||| |  |    ||  |  |||||||||||||||||||||| ||||| ||||||||||| || ||| || |||||||||||||||| ||||| || || ||||| ||| | |||||||| ||
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgt-tgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG

upper sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S336_7V6.1 (Physcomitrella patens), 3'ss of exon 4

---------------------------------------------------------------------------------------gtaagtacata-aacttcattgtttatgttctatccttcttctgtaa---tgatacttat-acttgattgcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAAT-AAAGCAGG
                                                                                       || | || |   |  || | | |||||  |  ||     |  || |    |  |||||   | ||   |||||| |||||||||||||| ||||||||||||||||| ||||| ||| |  |||| |||||||| ||||| ||  ||||||||||  | || ||| ||| |   
gtacgttgactgttttgaaccttgggtcatcttacgctataagagtttgtctgcgttcctaatttacagttagtttcgttttaggcagttaataaaagcagtttgaatatttat-ctagatggaagtattgaatcttttctacttgggaatttcgtgcagTGTACAAGAAGCACTATCCACCTGCCTTGAATGACGAGGTATGGCGCTTGGACAAGATTGGGAAGGACGGAGCCTTTCACAAGCGCCTCAATCAAAACCA-

upper sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S84_168V6.1 (Physcomitrella patens), 3'ss of exon 4

--------------------gtaagtacataaacttcattgtttatgttc--------tatccttct-tctgtaatgatacttatacttgat----tgcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG
                      ||||||  ||   ||| ||   || ||         ||   |||| | | |||  ||  || |   | |     |||||| ||||||||||||||||| ||| |||||||||||||||||||| || |||| || ||||||||||| ||| | ||||||||  | || ||| |  |  |
gcctttttacggtccctggaagaagtacg-aaggatcagtggaaatattaggaatggatacgtttctgtttctaagaatcgttgtcggtcacattctgcagTTTACAAGAAGCACTACCCGCCTTCCTTGAATGATGAGGTCTGGCGATTGGACAAAATTGGCAAGGACGGTGCTTTTCACAAGCGTCTCAATCAGTCTCG

upper sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S98_167V6.1 (Physcomitrella patens), 3'ss of exon 4

---------------------gtaagtacataaacttcattgtttat----gttctatccttcttctgtaa-tgatacttatacttgat-------tgcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG
                      |  || | | ||   | |  || |     |    ||| |   ||| ||  | ||| || |  ||| |       | |||| |||||||||||||| || ||||| || ||||| ||||| ||| || |||| |||||||| || || ||| | || |||||| | |||||| ||||| |
tgccctgtgcacatccattcgttctgtgc-tgaatgccgtgattaacagaagaaaaatcatatctctatatctaataattgttgttggtcaccttgtacagTCTACAAGAAGCACTATCCGCCTGCTTTAAATGACGAGGTTTGGCGATTGGACAAGATTGGAAAAGACGGTGCTTTCCACAAACGTCTAAATCAAGCAAG

upper sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4

--------------------------------gtaagta-cataa-acttcattgtttatgttctatccttcttctgtaatgatacttatacttgattgcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG
                                  | | | |||   |||| ||||  |     |  |     || | |  |  | || | ||||   |||||| ||||| |||||||||||||||||||||||||| ||||| ||| |  |||| |||||||| || |||||| | || |||||  | || ||| ||||   
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttct--ttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA

upper sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S34_132V6.1 (Physcomitrella patens), 3'ss of exon 4

-------------------------gtaagtacataaacttcattgtttatgttctatccttcttctgtaatgatacttatacttgattgc-------agTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG
                           ||| | | | |    || ||  | |  | |    |||    |  ||||  || |  |||||| |       ||| |||||||||||||| ||||| ||||||||||| ||||| ||| || |||| |||||||| || || ||| | || |||||  | |||||| ||||   
tctgccagatttccaagttgtgatcagaagaagaaagaagggatggtgaaagcccaacatatctgtatttttgattattgttgttgattactctgttcagTTTACAAGAAGCACTATCCACCAGCCTTGAATGACGAGGTTTGGCGATTGGACAAGATTGGGAAAGACGGTGCTTTCCACAAGCGTCTAAATCAAGCTCA

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|4260437|gb|AI416933.1|AI416933

EST:     TCGTGAAGCCAAAACAGAGGCCTTCACTGTTAAGGATCACCGTGGAGAAT                         TATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGG
genomic: TCGTGAAGCCAAAACAGAGGCCTTCACTGTTAAGGATCACCGTGGAGAATgtaagtacat ... ttgattgcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGG

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cttcattgtttatgttctatccttcttctgtaatgatacttatacttgattgcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG

                                           acttgat  putative branch site (score: 5)
                              taatgatacttata  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