ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGAAGAAGAACTTCTCCCTGGTGGGAGGGACATGCGTGTTACGAATGATAATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagattgtagtcatatcatttggatgcattggaaggctttgctaattgttttcctggtttctatcatag

Basic information

species	Zea mays
transcript	GRMZM2G101098_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G101098_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g06690.3 (Oryza sativa), 5'ss of exon 21

TGAAGAAGAACTTCTCCCTGGTGGGAGGGACATGCGTGTTACGAATGATAATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagattgtagtcatatcatttggatgcattggaaggctttgcta-attgttttcc----tggtttctatcatag
|||||||||||| ||||| |||||||| || |||||||| || | ||| ||||||||||||| |||||||||||| ||||| |||||||| ||||| ||||||| |  ||    |   | |||||||  ||  ||| ||  | ||| || ||  ||| ||    |  ||| ||||| ||
TGAAGAAGAACTGCTCCCAGGTGGGAGAGATATGCGTGTAACTAGTGAAAATGTTATTACTTATATCCATCTTGTCGCCAACCATCGGTTGAACTATCAGgtaatacaat----gcattgtcatttgcttgtcttgaaatacgttgatacataatttgccattgttttttttatcacag

upper sequence: GRMZM2G101098_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA09G03680.1 (Glycine max), 5'ss of exon 8

TGAAGAAGAACTTCTCCCTGGTGGGAGGGACATGCGTGTTACGAATGATAATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaa--aagat----tgtagtcatat-----------catttggatgca---ttggaaggctttgctaattgtttt---cctggtttctatcatag---
 ||||| || || || || || || | | || | ||||| || ||||| ||||| |||||||| ||||||||||| |||||||| || || || |  ||||||||  ||| |    | | |  | ||           || ||  ||  |   | ||||    |    |  |    |    |    || | || ||    
AGAAGAGGAGCTGCTTCCAGGGGGAAAGAACCTTCGTGTCACTAATGAGAATGTCATTACTTTCATCCATCTTGTGGCCAATCACCGCTTGAATTTTCAGgtaaagtaaggtctagtttggataaatttttaaataaacacttatatataggatgggaaaaaataaagaggtaaaatgagtcaaacttatctcttaaatt

upper sequence: GRMZM2G101098_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G36390.1 (Glycine max), 5'ss of exon 20

TGAAGAAGAACTTCTCCCTGGTGGGAGGGACATGCGTGTTACGAATGATAATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagattgtagtcatatcatttggatgcattggaaggctttgctaattgttttcctggtttctatcatag------------------------------
 || || ||||| || ||||| || ||| || ||||||| || ||||| ||||| ||||||||||| |||||||| |||||||| || || || |  ||||||||   | | |    |||  | |   ||  | | |||    ||||   ||||  | |   ||  ||  ||                                
AGAGGAGGAACTGCTTCCTGGAGGAAGGAACCTGCGTGTCACCAATGAAAATGTCATTACTTTTATTCATCTTGTAGCCAATCACCGCTTGAATTTTCAGgtaaagttactttttaaatagaaataaaataaaattgaa----ttgcatcttgtacttccaattcttagaatgtgggtttgggcctaactcgttccaaaagcta

upper sequence: GRMZM2G101098_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA17G04180.1 (Glycine max), 5'ss of exon 20

TGAAGAAGAACTTCTCCCTGGTGGGAGGGACATGCGTGTTACGAATGATAATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagattgtagtcatatcatttggat--gcattggaaggctttgctaattgtt--ttcctggtttctatcatag----------------------
 || || ||||| || || || || ||| || | ||||| || ||||| ||||| |||||||||||||| ||||| |||||||| || || || |  ||||||||     | |  | | || |  |  |     |||||| ||| |     | |     ||| | || | |    | |                      
AGAGGAGGAACTGCTTCCCGGAGGAAGGAACCTACGTGTCACTAATGAGAATGTCATTACTTTTATCCACCTTGTAGCCAATCACCGCTTGAATTTTCAGgtaaagttgctttttttaaataaaataaaataaaattggatggcatcttctactacaaattcttagtatgtggatttgtgcctaactcaactcccaaaag

upper sequence: GRMZM2G101098_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT3G17205.2 (Arabidopsis thaliana), 5'ss of exon 20

TGAAGAAGAACTTCTCCCTGGTGGGAGGGACATGCGTGTTACGAATGATAATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagattgtagtcatatc------atttggatgcattggaag--gctttgctaattgtt--ttcctggtttc-tatcatag----
 || ||||| || || || || ||    |||||||| ||||| ||||| |||||||| ||||| || ||||| ||| |||||||||||||||| |  ||||||    |     | | |  ||      || | |    |   || |   |  ||  |||       |  || | || | ||||      
AGAGGAAGAGCTACTTCCAGGGGGCCAAGACATGCGAGTTACAAATGAGAATGTTATAACTTTCATTCATCTGGTTTCCAATCATCGGTTAAATTTTCAGgtactggggaaccacttacctctcatttatcttggcatacctgaggtcaccctgtaaatcaacagctattgatatcatctcatttgcag

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|20811283|gb|BQ295761.1|BQ295761

EST:     ATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAG                         ATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCA
genomic: ATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagat ... tctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCA

EST: gi|6020745|gb|AW065553.1|AW065553

EST:     ATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAG                         ATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCA
genomic: ATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagat ... tctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCA

EST: gi|26456975|gb|CA828558.1|CA828558

EST:     ATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAG                         ATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCA
genomic: ATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagat ... tctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCA

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: 36

TGAAGAAGAACTTCTCCCTGGTGGGAGGGACATGCGTGTTACGAATGATAATGTTATTACTTTTATCCATCTTGTTGCCAATCATCGGTTAAACTACCAGgtaaaaagat ... tctatcatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAACAGCTTATACCAAAAGACTGGATTGATATGTTCAATGAACATGAAATTCAG

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 30

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 41