ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTGGGCAATTAATCTGATGGCCGATGTTGTAGAGCAAGAAAACTACAACAAGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAGgttaactgacacgcgtcttactatgtcttcagattatacaaggttcatattatacctacacatacgctaatcctggtgcatttctcttccag

Basic information

species	Zea mays
transcript	GRMZM2G114192_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G114192_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g48790.1 (Oryza sativa), 5'ss of exon 4

CTGGGCAATTAATCTGATGGCCGATGTTGTAGAGCAAGAAAACTACAACAAGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAGgttaactgacacgcgtcttactatgtcttcagattatacaaggttcatattatacctacacatacgctaatcctggtgcatttctcttccag
 ||||| || ||||||||||| |||||||| ||||| |||||||||||||||||||| ||  | |||||||| ||||| |||||||| || ||||||||||| |   || ||   |||    ||   |||   ||| | |||            | ||||||||| |||| ||||     ||| | ||||||
TTGGGCTATCAATCTGATGGCTGATGTTGTGGAGCATGAAAACTACAACAAGATGAATGCTAGAAACATCGCTATGGTCTTTGCGCCAAACATGACTCAGgt-attagaaacaactctgg--attctttcg--ttagaaaag------------catacacatacactaa-cctgcaatgtttgttttccag

upper sequence: GRMZM2G114192_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G44820.1 (Glycine max), 5'ss of exon 4

CTGGGCAATTAATCTGATGGCCGATGTTGTAGAGCAAGAAAACTACAACAAGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAGgttaactgacac-gcgtcttactatgtcttcagattatacaaggttcatattatacctacacatac-gctaatcctggtgcatt-tctcttccag---------
||||||||| ||| ||||||| |||||||| ||||  ||| | | |||||| ||||| || || ||  | || ||||||||||||||||| ||||| ||||||| |  |||         |   ||| |||   || |    | ||| | ||       | || || | | |  | ||  |||| | |  |  ||         
CTGGGCAATCAATTTGATGGCAGATGTTGTTGAGCGTGAACAGTTCAACAAAATGAATGCTCGCAATGTTGCCATGGTTTTTGCGCCCAACATGACACAGgttagccaacattataagcaaaggtgtattc---ttctgtt-gtttcgtgttggtttctctcaaacagtttaatcaggctcattatttagttgagcttccttat

upper sequence: GRMZM2G114192_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G42090.1 (Glycine max), 5'ss of exon 4

CTGGGCAATTAATCTGATGGCCGATGTTGTAGAGCAAGAAAACTACAACAAGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAGgttaactgacac-----gcgtcttactatgtcttcag--attatacaaggttcatattatacctacacatacgctaatcctggtgcatttct---cttccag
||||||||| ||| ||||||| || ||||| || || ||| | | |||||| ||||| || || || || || ||||||||||||||||| ||||| ||||||| |  |||      ||   | |  |||| |||     || |  |  |||  | |    |  |||  |    ||  |    |   |   |   |||||  
CTGGGCAATCAATTTGATGGCAGACGTTGTTGAACATGAACAGTTCAACAAAATGAATGCTCGCAATATTGCCATGGTTTTTGCGCCCAACATGACACAGgttagccaacattataagcaaataaagatgtattcttctgttgtttattgttggtttctctcaaacagtttaattaggctcattatttagttgaacttcc--

upper sequence: GRMZM2G114192_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv15s0048g02830.t01 (Vitis vinifera), 5'ss of exon 5

CTGGGCAATTAATCTGATGGCCGATGTTGTAGAGCAAGAAAACTACAACAAGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAGgttaactgacacgcgtcttactatgtcttcagattatacaa----ggttcatattatacctacacatacgctaatcctggtgc--atttctcttccag----
|||| | || ||| ||||| | ||||| ||  |||| ||| |  ||||||||||||| || || ||||| || ||||||||||| || || ||||||||||||   | |||    ||||  | |||| |    || ||       | | |||||      |  |||   | ||  |   ||||     || ||  | |    
CTGGACCATCAATTTGATGACAGATGTAGTGCAGCATGAACATCACAACAAGATGAATGCACGCAACATTGCAATGGTTTTTGCACCTAACATGACTCAGgttgcttaacat--atcttgttctgtcgttttgttttaaggttctgctacatatggggtatctacagttggtatccaatgtgctagcctcactagctgactt

upper sequence: GRMZM2G114192_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S13_243V6.1 (Physcomitrella patens), 5'ss of exon 4

CTGGGCAATTAATCTGATGGCCGATGTTGTAGAGCAAGAAAACTACAACAAGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAGgttaact------gacacgcgtctta----ctatgtcttcag-attatacaaggttcatattatac-ctacacat---------acgctaatcctggtgcatt-tctcttccag---------------
||||||  | ||| ||||||| ||||| ||  |  | |||     ||||||||||||||| || || || || ||||| ||||| || |||||||||||||| |         |||   |  |||     ||    ||| |  |  ||  | | ||  | ||  || || ||| |         |||||||     |   |    || || |                 
CTGGGCTGTCAATTTGATGGCTGATGTAGTCCAAGACGAAGTAGTCAACAAGATGAACGCTCGCAATATTGCAATGGTCTTTGCTCCTAATATGACTCAGgtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatatctgcag

upper sequence: GRMZM2G114192_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ22564 (Selaginella moellendorffii), 5'ss of exon 4

CTGGGCAATTAATCTGATGGCCGATGTTGTAGAGCAAGAAAACTACAACAAGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAGgttaactgacacgcgtcttactatgtcttcagattatacaaggttca-tattatacctacacatacgctaatcctggtgcatttctcttccag
||||||  | ||||| |||||||| || |   || | ||    |  |||||||||||| ||||||||||||| ||||||||||| ||||| |||||||||||    |    |   | | | |  ||  |  | || |      ||   | | ||   |   | |  |||   || |                 
CTGGGCGCTGAATCTCATGGCCGACGTCGCCCAGGAGGAGGCGTCAAACAAGATGAACTCCCGGAACATCGCAATGGTTTTTGCTCCCAACATGACTCAGgtacgtt----cctctttcatttggtgcttggtttttgttttcttttctgtaatgtatttccttttgctgtcccag-----------------

upper sequence: GRMZM2G114192_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ12967 (Selaginella moellendorffii), 5'ss of exon 4

CTGGGCAATTAATCTGATGGCCGATGTTGTAGAGCAAGAAAACTACAACAAGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAGgttaactgacacgcgtcttactatgtcttcagattatacaaggttca-tattatacctacacatacgctaatcctggtgcatttctcttccag
||||||  | ||||| |||||||| || |   || | ||    |  |||||||||||| ||||||||||||| ||||||||||| ||||| |||||||||||    |    |   | | | |  ||  |  | || |     |||   | | ||   |   | |  |||   || |                 
CTGGGCGCTGAATCTCATGGCCGACGTCGCCCAGGAGGAGGCGTCAAACAAGATGAACTCCCGGAACATCGCAATGGTTTTTGCTCCCAACATGACTCAGgtacgtt----cctctttcatttggttcttggtttttgttttgttttctgtaatgtatttccttttgctgtcccag-----------------

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|211225804|gb|FL287503.1|FL287503

EST:     AGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAG                         ATGGCCGATCCGTTAACTGCCCTGATACATGCGGTTCAGGTGATGAATTTC
genomic: AGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAGgttaactgac ... tctcttccagATGGCCGATCCGTTAACTGCCCTGATACATGCGGTTCAGGTGATGAATTTC

EST: gi|71299638|gb|DR785827.1|DR785827

EST:     AGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAG                         ATGGCCGATCCGTTAACTGCCCTGATACATGCGGTTCAGGTGATGAATTTC
genomic: AGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAGgttaactgac ... tctcttccagATGGCCGATCCGTTAACTGCCCTGATACATGCGGTTCAGGTGATGAATTTC

EST: gi|78089387|gb|DV517761.1|DV517761

EST:     AGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAG                         ATGGCCGATCCGTTAACTGCCCTGATACATGCGGTTCAGGTGATGAATTTC
genomic: AGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAGgttaactgac ... tctcttccagATGGCCGATCCGTTAACTGCCCTGATACATGCGGTTCAGGTGATGAATTTC

EST: gi|16379323|gb|BI992874.1|BI992874

EST:     TTTTTGCGCCCAATATGACTCAG                         ATGGCCGATCCGTTAACTGCCCTGATACATGCGGTTCAGGTGATGAATTTC
genomic: TTTTTGCGCCCAATATGACTCAGgttaactgac ... tctcttccagATGGCCGATCCGTTAACTGCCCTGATACATGCGGTTCAGGTGATGAATTTC

EST: gi|76017793|gb|DT944963.1|DT944963

EST:     AGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAG                         ATGGCCGATCCGTTAACTGCCCTGATACATGCGGTTCAGGTGATGAATTTC
genomic: AGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAGgttaactgac ... tctcttccagATGGCCGATCCGTTAACTGCCCTGATACATGCGGTTCAGGTGATGAATTTC

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: 44 (upstream exon), 43 (downstream exon)
Score: 16

CTGGGCAATTAATCTGATGGCCGATGTTGTAGAGCAAGAAAACTACAACAAGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAGgttaactgac ... tctcttccagATGGCCGATCCGTTAACTGCCCTGATACATGCGGTTCAGGTGATGAATTTCCTCAAGACCTTAATCTTGAAGACTCTAAAGGAACGAAACAAAAAGGATG

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 21

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 68