ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CCCCAGGTCCGGCGCCGCCACCTCGTTTCTCGAGCGCCGCGAGTCGGAGCGCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATGgtgcgactgtttccgtttcccaactctcttcaactattccgcgccgtgcagtgttcatttgggtggtgaccccacgtcgagaatttgtgcaatccgtgatgttctgatttttgaaagctctgctactgaagacacttaagttttgtttgcttgttcatgtttcgattcgtag

Basic information

species	Zea mays
transcript	AC182617.3_FGT001
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC182617.3_FGT001 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os12g37960.1 (Oryza sativa), 5'ss of exon 1

CCCCAGGTCCGGCGCCGCCACCTCGTTTCTCGAGCGCCGCGAGTCGGAGCGCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATGgtgcgactgtttccg---tttcccaactctcttcaactattccgcgccgtgcagtgttcatttgggtggtgaccccacgtcgagaatttgtgcaatccgtgatgttctgatttttgaaagctctgctactgaagacact-taagttttgt---ttgcttgttcatgtttcgattcgtag-------
||||||||| | ||||||| || |||| |||||||||||||||||||||||||| |||||||| ||||| ||||||||||| || ||||||||||| ||||||||||   || |      | |||  || |||    ||   | ||   ||  |  | | ||    |  |     | | |    |||  || |  | |||  ||  |  |||   | |  ||||||| ||  |||| |  | | || |||   ||  |  || |   || ||||  |         
CCCCAGGTCGGCCGCCGCCGCCGCGTTCCTCGAGCGCCGCGAGTCGGAGCGCGCCCTCCACTTCGTCAAGTACCAGGGCCTTGGGAACGACTTCATCATGgtgcgacgccttactagcgcttccatttcacttttcttagaac-cgatttgttgcttcccttcaatttttttaatcccctttgtaatcagt-cgcttcgtc-tgcacgaattagagcagtctctgctgctttagacgcggtgatttctgtatttttttgatttagtcttggattttttttcttcag

upper sequence: AC182617.3_FGT001 (Zea mays), 5'ss of exon 1
lower sequence: AT3G53580.1 (Arabidopsis thaliana), 5'ss of exon 1

CCCCAGGTCCGGCGCCGCCACCT-CGTTTCTCGAGCGCCGCGAGTCGGAGCGCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATGgtgcgactgttt-ccgtt---tcccaactctcttcaactattccgcgccgtgcagtgttcatttgggtggtgaccccacgtcgagaatttgtgcaatccgtgatgttctgatttttgaaagctctgctactgaagacacttaagttttgtttgcttgttcatgtttcgattcgtag
 | ||| |  |       | ||  ||  | |      |    |        | | ||| |||||||| |||||||| ||||||||||| ||||||||  |||| |   ||||  |||||   | |  | | |  | |  ||  |||    ||   |  ||| |     || |     ||  |      | | || |||    ||| || |                                                                   
-CACAGCTGAGAAATTTTCTCCGGCGAGTTTTCTAGACAAAAAAGAAACCGGAGTTCTTCACTTTGTGAAATACCATGGCCTCGGCAATGACTTCATTTTGgtacttttgttcaccgttgaattctcaatttggtaatttaacccgaaatgtatcgaattcttacaaatgtt---ttcaaatttttcgtctttggaattg--gattttgtag-----------------------------------------------------------------

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|149103897|gb|EE289312.2|EE289312

EST:     GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG
genomic: GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATGgtgcgactgt ... cgattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG

EST: gi|148932662|gb|EC876592.2|EC876592

EST:     GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG
genomic: GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATGgtgcgactgt ... cgattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG

EST: gi|149014406|gb|EE044007.2|EE044007

EST:     GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG
genomic: GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATGgtgcgactgt ... cgattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG

EST: gi|74235623|gb|DT643537.1|DT643537

EST:     GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG
genomic: GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATGgtgcgactgt ... cgattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG

EST: gi|71757461|gb|DR955398.1|DR955398

EST:     GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG
genomic: GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATGgtgcgactgt ... cgattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG

EST: gi|148930368|gb|EE284809.2|EE284809

EST:     GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG
genomic: GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATGgtgcgactgt ... cgattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG

EST: gi|71432546|gb|DR813596.1|DR813596

EST:     GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG
genomic: GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATGgtgcgactgt ... cgattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG

EST: gi|50325885|gb|CO521011.1|CO521011

EST:     GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATG                         GTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG
genomic: GCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATGgtgcgactgt ... cgattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCG

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: 48 (upstream exon), 49 (downstream exon)
Score: 430

CCCCAGGTCCGGCGCCGCCACCTCGTTTCTCGAGCGCCGCGAGTCGGAGCGCGCTCTCCACTTTGTCAAATACCAGGGCCTCGGCAACGACTTCATAATGgtgcgactgt ... cgattcgtagGTGGACAACAGGGATTCGTCGGTGCCGAAGGTGACGCCCGAGGAGGCTGCGAAGCTGTGCGACCGAAACTTCGGCATTGGCGCCGACGGTGTTATCTTCG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 377

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 420