ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CACCTTGATCAGGAAGGTATTAGTTTTTGCTGTCGAACAACTTATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttcccatctgtgttactaaagatgctaccttaccatacacatatttattctaattctgtttttgcacccccag

Basic information

species	Zea mays
transcript	GRMZM2G109039_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G109039_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 7

CACCTTGATCAGGAAGGTATTAGTTTTTGCTGTCGAACAACTTATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttcccatctgtgttactaa-------agatgctaccttaccatacacatatttattctaattctgtttttgcacccccag
||||||||||  ||||| ||||| |||||||||||||| || |||||||| || |||||||| ||||| ||||||||||| |||||  | |||||| | ||    | |||||  ||       |||||  |||||     ||    || | |  |||| |||||||   | ||||||
CACCTTGATCGAGAAGGAATTAGCTTTTGCTGTCGAACTACATATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgccttgttctgttataaagttcattagatgtgacctttttgaacttgcatctgtattaatactgtttt---atccccag

upper sequence: GRMZM2G109039_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA04G12500.1 (Glycine max), 5'ss of exon 7

CACCTTGATCAGGAAGGTATTAGTTTTTGCTGTCGAACAACTTATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaact--tcccatctgtgttactaaagatgctaccttacc-----atacacatatttattctaattc---tgtttttgcacccccag
||||| ||||     ||| |||| ||||||    ||||||||||||||||||||||||| || |||||  ||||||| | | ||    |||||||  |  |      | |  |  |     ||  |  | |       |||     |   | | ||||     ||||||   |     ||
CACCTAGATCGACCTGGTGTTAGCTTTTGCACGAGAACAACTTATGATGATAATGCTATCACCAATGCCATTGAGATTTATGATTGTCCTAGgtatatagttttccttctcctggtggttttgtcatttgatttatggatatcggcaccaagtttaatgtgattgttttctgatttttag

upper sequence: GRMZM2G109039_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv00s0568g00010.t01 (Vitis vinifera), 5'ss of exon 7

CACCTTGATCAGGAAGGTATTAGTTTTTGCTGTCGAACAACTTATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttcccatctgtgttactaaagatgctaccttaccatacacatatttattctaatt---ctgtttttgcaccc---ccag
 |  | ||||     ||  || | ||||| | ||||||||||||||| || |||||||| |||||||| || ||||| | | |||   | ||||   ||   |||| |  |  ||  | || ||   ||    | |  ||  ||    |  |    ||   |   |      ||||
TATTTAGATCGACCTGGAGTTTGCTTTTGTTCTCGAACAACTTATGACGACAATGCTATCACAAATGCAGTAGAGATTTATGATAGTCCCAGgttgtttattatcttttgttgtagtggtggtaaagtaattcatatctaaatacaggagctgacttgagctaaaattttgtccag

upper sequence: GRMZM2G109039_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv00s1206g00020.t01 (Vitis vinifera), 5'ss of exon 3

CACCTTGATCAGGAAGGTATTAGTTTTTGCTGTCGAACAACTTATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttcccatctgtgttactaaagatgctaccttaccatacacatatttattctaatt---ctgtttttgcaccc---ccag
 |  | ||||     ||  || | ||||| | ||||||||||||||| || |||||||| |||||||| || ||||| | | |||   | ||||   ||   |||| | ||  ||  | || ||   ||    | |  ||  ||    |  |    ||   |   |      ||||
TATTTAGATCGACCTGGAGTTTGCTTTTGTTCTCGAACAACTTATGACGACAATGCTATCACAAATGCAGTAGAGATTTATGATAGTCCCAGgttgtttattatctttttttgtagtggtgttaaagtaattcatatctaaatacaggagctgacttgagctaaaattttgtccag

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|211395430|gb|FL283720.1|FL283720

EST:     ATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAG                         TGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA
genomic: ATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttccc ... gcacccccagTGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA

EST: gi|22472113|gb|BU036593.1|BU036593

EST:     TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAG                         TGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA
genomic: TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttccc ... gcacccccagTGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA

EST: gi|58029875|gb|CX725302.1|CX725302

EST:     TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAG                         TGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA
genomic: TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttccc ... gcacccccagTGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA

EST: gi|60347828|gb|DN214801.1|DN214801

EST:     TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAG                         TGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA
genomic: TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttccc ... gcacccccagTGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA

EST: gi|8368895|gb|BE051840.1|BE051840

EST:     TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAG                         TGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA
genomic: TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttccc ... gcacccccagTGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA

EST: gi|453303|gb|T15277.1|T15277

EST:     TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAG                         TGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA
genomic: TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttccc ... gcacccccagTGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA

EST: gi|67012835|gb|CO441584.1|CO441584

EST:     TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAG                         TGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA
genomic: TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttccc ... gcacccccagTGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA

EST: gi|20301275|gb|BQ164218.1|BQ164218

EST:     TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAG                         TGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA
genomic: TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttccc ... gcacccccagTGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA

EST: gi|26456084|gb|CA827667.1|CA827667

EST:     TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAG                         TGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA
genomic: TATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttccc ... gcacccccagTGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTA

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), 49 (downstream exon)
Score: 504

CACCTTGATCAGGAAGGTATTAGTTTTTGCTGTCGAACAACTTATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttccc ... gcacccccagTGGCGCCGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTATGACATGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 686

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 601