ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

gtccatatgcatcccctccttccttcctcttccttctatctgctatggctgctgccccaccggtctaatgacgcgcagcgatttctgaccatcccctgacggtttgcggtggccgtccaaatccaatcccagGCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTATCCCCCATCGCGGTTCGCGGCGCAGGCCCACGCCTTCGCCGTCCTCTCCG

Basic information

species	Zea mays
transcript	GRMZM2G039577_T03
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G039577_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S14_318V6.2 (Physcomitrella patens), 3'ss of exon 1

----------------------------------------------------gtccatatgcatcccctccttccttcctcttccttc-tatctgctatggctgctgccccaccggtctaatgacgcgcagcgatttctgaccatcccctgacggtttg--cggtggccgtccaaatccaa---------tcccagGCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTATCCCCCATCGCGGTTCGCGGCGCAGGCCCACGCCTTCGCCGTCCTCTCCG
                                                    ||   |  | || |  |  |    | |   || |   | |||| | ||  |  | |   || |   | ||   | | |||  | |  |  |||     |  |||      ||  || ||  ||    |          |  |||||||||||| ||||| |||||||||| ||||||||| |||| || || ||| | ||  |  ||||    || || ||  | ||  |   | |  | | ||
gtaagtggaacatgggacgtagtgtattagggttatttgtaggtgcgaattggtttcttaggattcagtgatagtctgccgatcttgaatttctggtttgtttttttcgttactgagttgattgaggg-agcactgtgcgtgcatttttggtgggtagagttggaagctgttgaacgttatatgggtgttttacagGCGACCATGGTCTGCATGGACAACTCAGAGTGGATGCGGAACGGCGATTATTCACCTACTAGGTTTCAAGCTCAAGCTGATGCTATAAACCTGATTTGCG

upper sequence: GRMZM2G039577_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S14_318V6.1 (Physcomitrella patens), 3'ss of exon 1

gtccatatgcatcccctccttccttcctcttccttctatctgctatggctgctgccccaccggtctaatgacgcgcagcgatttctgaccatccc--ctgacggtttgcggtggccgtccaaatccaatcccagGCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTATCCCCCATCGCGGTTCGCGGCGCAGGCCCACGCCTTCGCCGTCCTCTCCG
                             ||  || | |  | ||  |  | ||    |  |    |     | ||    |||| ||           ||   | |   |   |   |     |    |  |||||||||||| ||||| |||||||||| ||||||||| |||| || || ||| | ||  |  ||||    || || ||  | ||  |   | |  | | ||
----------------------------gtttgtttttttcgttactga-gttg----attgagggagcactgtgcgtgcatttttggtgggtagagttggaagctgttgaacgttatatgggtgtt-ttacagGCGACCATGGTCTGCATGGACAACTCAGAGTGGATGCGGAACGGCGATTATTCACCTACTAGGTTTCAAGCTCAAGCTGATGCTATAAACCTGATTTGCG

upper sequence: GRMZM2G039577_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ17485 (Selaginella moellendorffii), 3'ss of exon 1

gtccatatgcatcccctccttccttcctcttccttctatctgctatggctgctgccccaccggtctaatgacgcgcagcgatttctgaccatcccctgacggtttgcggt-ggccgtccaaatccaatcccagGCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTATCCCCCATCGCG---GTTCGCGGCGCAGGCCCACGCCTTCGCCGTCCTCTCCG
                                                                                     | | |  | |  ||   ||  ||   ||||   |   ||   | ||||||||| ||||||||| | ||||| || ||||||||| | |||||||||||    ||  || |    |||  | | || ||  | ||  ||    |  |||   
------------------------------------------------------------------------------------gtaagctcctcgcgatctttcacgccaggcctatcttctcttgtgccagGCGACGATGATCTGCATAGACAATTCCGAGTGGATGCGAAATGGGGACTACTATCCGACGAGTAGATTCCAGTCCCAAGCTGATGCTGTCAATCTTATCT---

upper sequence: GRMZM2G039577_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ28815 (Selaginella moellendorffii), 3'ss of exon 1

gtccatatgcatcccctccttccttcctcttccttctatctgctatggctgctgccccaccggtctaatgacgcgcagcgatttctgaccatcccctgacggtttgcggt-ggccgtccaaatccaatcccagGCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTATCCCCCATCGCG---GTTCGCGGCGCAGGCCCACGCCTTCGCCGTCCTCTCCG
                                                                                     | | |  | |  ||   ||  ||   ||||   |   ||   | ||||||||| ||||||||| | ||||| || ||||||||| | |||||||||||    ||  || |    |||  | | || ||| | ||  ||    |  |||   
------------------------------------------------------------------------------------gtaagctcctcgcgatctttcacgccaggcctatcttctcttgtgccagGCGACGATGATCTGCATAGACAATTCCGAGTGGATGCGAAATGGGGACTACTATCCGACGAGTAGATTCCAGTCCCAAGCCGATGCTGTCAATCTTATCT---

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|149080349|gb|EE169366.2|EE169366

EST:     GAACCCACCACCTCGCCGCCCGCCACCAGCCCACCACCATGGTGCTCGAG                         GCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTAT
genomic: GAACCCACCACCTCGCCGCCCGCCACCAGCCCACCACCATGGTGCTCGAGgtccatatgc ... ccaatcccagGCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTAT

EST: gi|211080675|gb|FL094853.1|FL094853

EST:     GAACCCACCACCTCGCCGCCCGCCACCAGCCCACCACCATGGTGCTCGAG                         GCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTAT
genomic: GAACCCACCACCTCGCCGCCCGCCACCAGCCCACCACCATGGTGCTCGAGgtccatatgc ... ccaatcccagGCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTAT

EST: gi|148934661|gb|EC878710.2|EC878710

EST:     GAACCCACCACCTCGCCGCCCGCCACCAGCCCACCACCATGGTGCTCGAG                         GCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTAT
genomic: GAACCCACCACCTCGCCGCCCGCCACCAGCCCACCACCATGGTGCTCGAGgtccatatgc ... ccaatcccagGCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTAT

EST: gi|148959615|gb|EC905557.2|EC905557

EST:     GAACCCACCACCTCGCCGCCCGCCACCAGCCCACCACCATGGTGCTCGAG                         GCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTAT
genomic: GAACCCACCACCTCGCCGCCCGCCACCAGCCCACCACCATGGTGCTCGAGgtccatatgc ... ccaatcccagGCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTAT

EST: gi|211080674|gb|FL094852.1|FL094852

EST:     GAACCCACCACCTCGCCGCCCGCCACCAGCCCACCACCATGGTGCTCGAG                         GCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTAT
genomic: GAACCCACCACCTCGCCGCCCGCCACCAGCCCACCACCATGGTGCTCGAGgtccatatgc ... ccaatcccagGCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTAT

EST: gi|78083985|gb|DV512378.1|DV512378

EST:     GAACCCACCACCTCGCCGCCCGCCACCAGCCCACCACCATGGTGCTCGAG                         GCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTAT
genomic: GAACCCACCACCTCGCCGCCCGCCACCAGCCCACCACCATGGTGCTCGAGgtccatatgc ... ccaatcccagGCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTAT

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 3 RNA-Seq libraries.

Block sizes: 45 (upstream exon), 37 (downstream exon)
Score: 7

CACATAGTCACGTTTCCGTCTTCCGAAGCAGCACGTCCGCTCGCCTCCGAGAACCCACCACCTCGCCGCCCGCCACCAGCCCACCACCATGGTGCTCGAGgtccatatgc ... ccaatcccagGCGACCATGATCTGCGTGGACAACTCGGAGTGGATGAGGAATGGGGACTATCCCCCATCGCGGTTCGCGGCGCAGGCCCACGCCTTCGCCGTCCTCTCCG

Block sizes: 13 (upstream exon), 37 (downstream exon)
Score: 1