ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgccctgctcatttatctcgtggatgacttgaaaaaaaacgaggtttggattctgggactctgcattcgtacgtgttgacatggatcttgttgcttctgtacgtgcag

Basic information

species	Zea mays
transcript	GRMZM2G026470_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G026470_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 5'ss of exon 6

ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgccctgctcatttatctcgtggatgacttgaaaaaaaacgaggtttggattctgggactctgcattcgtacgtgttgacatggatcttgttgcttctgtacgtgcag
|||||||||| |||||||||||||| || ||||| |||||| |||| ||  |  | || || ||||| ||||||||||| ||||||    | |||   |||||    |     |||  || | |  | | | ||| |  |  ||    ||     ||  |  ||||| | |   |   |                  
ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCTTGCCTGCTCCGACAGCTCGTGAAGCAATCCAGTACTCTATgtaa----gtcctaaacattt--tgcagcattgatgtgcatattacc-atgttggattgttgatgttcgatgatccaatttgttgtcttattttcag------------------

upper sequence: GRMZM2G026470_T01 (Zea mays), 5'ss of exon 6
lower sequence: EDP02064 (Chlamydomonas reinhardtii), 5'ss of exon 4

--------------ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgccctgctcatttatct----cgtggatgacttgaaaaaaaacgaggtttggatt--ctgggactctgcattcgtacgtgttgacatggatcttgttgcttctgtacgtgcag
              |||||||||||||| |||||||||||| |||  |||||||||||   || |  |  |||    | |   || || ||||  ||   || |||   || ||           ||||| |    || | ||   | |||   || |   | |  |    ||||      || | | |   || | |                   
GTTCTTCGAGGACTACAAGAAGAACGAGCACAAGGAGGTGGTCGTGGACGACTTCCTGGGTGCTGAGGAGGCCAAGAAGGTGGTCAAGGACTCGCTGgtgagacgcagggcgcagcggcgaggggcgtgggttgtgtgcagaatggc-aggccagggtcagccgcaagctagcatcgtcgtgtttagtcccagaacgt-------------------

upper sequence: GRMZM2G026470_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ33440 (Selaginella moellendorffii), 5'ss of exon 7

ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaa---gtcgccctgctc---attta-tctcgtggatgacttgaaaaaaaacgaggtttggattctgggactctgcattcgtacgtgttgacatggatcttgttgcttctgtacgtgcag
||||||||||||||||||||   ||||| || |||||||||||||| || |     |||    | || |||||| | ||||||| |    |  | | ||      ||  | ||||       |    | |||| || ||  |       ||   |||||| |   |  |                                   
ACAAGAAGAACGAGAACAAGACCGTGGCTGTGAACGACTTCCTGCCAGCAGAAAACGCCGTGCAGGCGATCCAGCATTCCATgtgagtgtggggacttgagtgggatacactctcactcgctagcgtagaaaacactagactaaagccgtgattctctgcttgtttcag-----------------------------------

upper sequence: GRMZM2G026470_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ27219 (Selaginella moellendorffii), 5'ss of exon 7

ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaa---gtcgccctgctc---attta-tctcgtggatgacttgaaaaaaaacgaggtttggattctgggactctgcattcgtacgtgttgacatggatcttgttgcttctgtacgtgcag
||||||||||||||||||||   ||||| || |||||||||||||| || |     |||    | || |||||| | ||||||| |    |  | | ||      ||  | ||||       |    | |||| || ||  |       ||   || ||| |   |  |                                   
ACAAGAAGAACGAGAACAAGACCGTGGCGGTGAACGACTTCCTGCCAGCAGAAAACGCCGTGCAGGCGATCCAGCATTCCATgtgagtgtggggacttgagtgggatacactctcactcgctagcgtagaaaacactagactaaagccgtgattctttgcttgtttcag-----------------------------------

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|71331881|gb|DR802819.1|DR802819

EST:     ACGACTTTCTGCCCCGCGGC-GCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTA
genomic: ACGACTTCCTGCCC-GCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTA

EST: gi|78023075|gb|DV491462.1|DV491462

EST:     AATGACTTCTTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC

EST: gi|28984521|gb|BQ539133.2|BQ539133

EST:     AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC

EST: gi|71331880|gb|DR802818.1|DR802818

EST:     AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC

EST: gi|62550248|gb|DN830668.1|DN830668

EST:     AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGT-TC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC

EST: gi|78121801|gb|DV540185.1|DV540185

EST:     AACGACTTCCTGCCCGCCGCCGCTGCCCGGGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC

EST: gi|84908555|gb|DW404433.1|DW404433

EST:     AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGT-TC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC

EST: gi|5499294|gb|AI855161.1|AI855161

EST:     AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC

EST: gi|60354156|gb|DN221129.1|DN221129

EST:     AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT                         GGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC
genomic: AACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTC

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 4 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 15

ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCATgtaaagtcgc ... gtacgtgcagGGACCTGTACGGCCAGTACATCATGCAGACCCTGCGGCGGTAGAGCGTGTCCTACCAGATCCCATGCGAGCTGAGCTGACGCAAGAGCACAGATCGACAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 362