ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATGTGGACCCTCCTTGACGTCTTCTTCTTCGGGAAGCCGTCGGTGATCGGTGCTGTGCAGGGCATGATCACCGGCCTTGTGTGCATCACGCCTGGCGCAGgtcagtagagtagccttgcctttctcttcgctccattggcagatggactccctaatactaacaaattatataagttgtgcaacttgcactggttggtaat...

Basic information

species	Zea mays
transcript	GRMZM2G043193_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G043193_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g34580.1 (Oryza sativa), 5'ss of exon 3

ATGTGGACCCTCCTTGACGTCTTCTTCTTCGGGAAGCCGTCGGTGATCGGTGCTGTGCAGGGCATGATCACCGGCCTTGTGTGCATCACGCCTGGCGCAGgtcagtagagtagccttgcctttctcttcgctccattggcagatggactccctaa--tactaacaaattatataagttgtgcaacttgcactggttggtaat----------
 |||||||  |||| || |||||||||||||||||||| ||||| || || || ||||||||||||||||| ||||| || |||||||| ||||| ||||||     ||| |||||  |||| |||       |||| |||| ||||||  || |  ||  | |||    |  || |  ||||| |||||   ||   |  |          
GTGTGGACAATCCTGGATGTCTTCTTCTTCGGGAAGCCATCGGTAATTGGCGCGGTGCAGGGCATGATCACTGGCCTGGTATGCATCACCCCTGGTGCAGgt-----gagaagcctccccttcctc-------cattagcaggtggactagctcagctaagaccaaccccttaaaatattgcaatttgcatcagtaccttgtcaccatagga

upper sequence: GRMZM2G043193_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S30_275V6.1 (Physcomitrella patens), 5'ss of exon 2

ATGTGGACCCTCCTTGACGTCTTCTTCTTCGGGAAGCCGTCGGTGATCGGTGCTGTGCAGGGCATGATCACCGGCCTTGTGTGCATCACGCCTGGCGCAGgtcagt-agagtagccttgcctttctcttcgctccattggcagatggactccctaatactaacaaattatataagttgtgcaacttgcactggttggtaat-----------------------
|  |||||   | | ||||| ||||||||||| ||||| || || || |||||||||||||| ||||| ||||  ||||||   || || ||||  |||||  ||| |    |      |     |  | ||| ||      |||| | |  | | || |   |     |||  |  ||||| |       | |   | |                        
ACATGGACTACCTTGGACGTGTTCTTCTTCGGCAAGCCTTCTGTCATTGGTGCTGTGCAGGGAATGATGACCGATCTTGTGGTTATTACACCTGCTGCAGgcaagtcatcacaatacaactgcaattgtggctgcagaacttgatgcaatggc-actatttggaggcc-tatt-gcagtgcatccgaggtcgatgatttaaatttcattcaatgtggtgtgcag

upper sequence: GRMZM2G043193_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S4_201V6.1 (Physcomitrella patens), 5'ss of exon 3

ATGTGGACCCTCCTTGACGTCTTCTTCTTCGGGAAGCCGTCGGTGATCGGTGCTGTGCAGGGCATGATCACCGGCCTTGTGTGCATCACGCCTGGCGCAGgtcagtagagtagccttgcctttctcttcgctccattggcagatggactccctaatactaacaaatt---------atataagttgtgcaacttgcactggttggtaat----------------------
 |||||||  |||| |||||  |  |||| ||||| || || ||||||||||| |||||||| |||||||| || |||||   |||||| ||||| |||||| | |  |||| |      | |   ||  ||   |     |||  |  |  ||     |   ||||         ||  |  || |||| ||   |||  ||   | |                      
GTGTGGACTTTCCTGGACGTGGTTGTCTTTGGGAAACCTTCCGTGATCGGTGCAGTGCAGGGAATGATCACGGGTCTTGTCGTCATCACCCCTGGTGCAGgt-aatttagtatctgcaattattagttaactgtgtctaatgatttatcctgtacggaaactgaattgatcgccacatcaagcttttgcagctctgactcatttccactgaacttttcttttgttttgcag

upper sequence: GRMZM2G043193_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S109_32V6.1 (Physcomitrella patens), 5'ss of exon 4

ATGTGGACCCTCCTTGACGTCTTCTTCTTCGGGAAGCCGTCGGTGATCGGTGCTGTGCAGGGCATGATCACCGGCCTTGTGTGCATCACGCCTGGCGCAGgtcagtagagtagccttgcctttctcttcgctcca---ttggcagatggac----tccctaatactaacaaattatataagttgtgc---aacttgcactggttggtaat---------------------------
 | |||||   | | || ||  |  ||||||| ||||| || ||||||||||| || ||||| |||||||| ||||||||   ||| || || |  |||||| |  |   ||     | || |||   ||| |||     |  || | ||     |||   ||  | ||   || |   | |||      ||||    ||  ||  | |                            
GTATGGACGTGCTTGGATGTGCTTGTCTTCGGCAAGCCTTCAGTGATCGGTGCGGTTCAGGGAATGATCACGGGCCTTGTTGTCATTACTCCCGCTGCAGgtgaccaacctaa----gtctctcttgacgcaccagaacagaaagtttgatctcatcctccatgttgacg--ttgtgccaattgcattcgaactcctgctcatttctgacattgttactttcaatgcaatcactcag

upper sequence: GRMZM2G043193_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S15_321V6.1 (Physcomitrella patens), 5'ss of exon 2

ATGTGGACCCTCCTTGACGTCTTCTTCTTCGGGAAGCCGTCGGTGATCGGTGCTGTGCAGGGCATGATCACCGGCCTTGTGTGCATCACGCCTGGCGC-----AGgtcagtagagtagccttgcctttctcttcgctc---cattggcag--atggactccctaatactaacaaattatataagttgtgcaacttgcactggttggtaat---------------------------------------------------------------------------
| ||||||   ||| |||||| || ||||||||||||| || || ||||| |||||||| |||||||| || || ||||||   || || || |  ||     |||||   || |   | ||  |  |||| | |      | ||   |   ||| | |  |  |  | |||| ||   ||  | |        |||||   ||  ||||                                                                           
ACGTGGACTACCCTGGACGTCATCGTCTTCGGGAAGCCATCAGTCATCGGCGCTGTGCAAGGCATGATGACGGGGCTTGTGATGATTACCCCCGCTGCTGgtaaggtccagagggagacattttccatctcattgtggggaccttaatatttatgcattttccgaaccaaacagatcgaatggggtagttctgctgcacaacttaataatgtgatgctgcttgaatttggattctgcgggaatctgtcccgtgtgttgagaggtgtgtgtaaattgtcggtgcag

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|71307661|gb|DR790050.1|DR790050

EST:     TGCTGTGCAGGGCATGATCACCGGCCTTGTGTGCATCACGCCTGGCGCAG                         GCCTGGTGCAAGGGTGGGCAGCCATTGTCATGGGAATTCTCTCAGGTAGCA
genomic: TGCTGTGCAGGGCATGATCACCGGCCTTGTGTGCATCACGCCTGGCGCAGgtcagtagag ... tattcaatagGCCTGGTGCAAGGGTGGGCAGCCATTGTCATGGGAATTCTCTCAGGTAGCA

EST: gi|18661149|gb|BM501241.1|BM501241

EST:     TGCTGTGCAGGGCATGATCACCGGCCTTGTGTGCATCACGCCTGGCGCAG                         GCCTGGTGCAAGGGTGGGCAGCCATTGTCATGGGAATTCTCTCAG-TAGCA
genomic: TGCTGTGCAGGGCATGATCACCGGCCTTGTGTGCATCACGCCTGGCGCAGgtcagtagag ... tattcaatagGCCTGGTGCAAGGGTGGGCAGCCATTGTCATGGGAATTCTCTCAGGTAGCA

EST: gi|71773597|gb|DR971495.1|DR971495

EST:     TGCTGTGCAGGGCATGATCACCGGCCTTGTGTGCATCACGCCTGGCGCAG                         GCCTGGTGCAAGGGTGGGCAGCCATTGTCATGGGAATTCTCTCAGGTAGCA
genomic: TGCTGTGCAGGGCATGATCACCGGCCTTGTGTGCATCACGCCTGGCGCAGgtcagtagag ... tattcaatagGCCTGGTGCAAGGGTGGGCAGCCATTGTCATGGGAATTCTCTCAGGTAGCA

EST: gi|149101228|gb|EE187339.2|EE187339

EST:     TGCTGTGCAGGGCATGATCACCGGCCTTGTGTGCATCACGCCTGGCGCAG                         GCCTGGTGCAAGGGTGGGCAGCCATTGTCATGGGAATTCTCTCAGGTAGCA
genomic: TGCTGTGCAGGGCATGATCACCGGCCTTGTGTGCATCACGCCTGGCGCAGgtcagtagag ... tattcaatagGCCTGGTGCAAGGGTGGGCAGCCATTGTCATGGGAATTCTCTCAGGTAGCA

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: 43 (upstream exon), 41 (downstream exon)
Score: 5

ATGTGGACCCTCCTTGACGTCTTCTTCTTCGGGAAGCCGTCGGTGATCGGTGCTGTGCAGGGCATGATCACCGGCCTTGTGTGCATCACGCCTGGCGCAGgtcagtagag ... tattcaatagGCCTGGTGCAAGGGTGGGCAGCCATTGTCATGGGAATTCTCTCAGGTAGCATCCCCTGGTACACTATGATGGTACTGCACAAGAAATGGTCCTTCATGCA

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 10