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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaataacatggatcacccattgttcttgtatcccatcattactttgaacaaactttaatttaccagtatctgcaatactccttgtgcag

Basic information

species Zea mays
transcript GRMZM2G065012_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065012_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g57350.1 (Oryza sativa), 5'ss of exon 9
AGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaa-acaataacat---ggatcacccattgttcttgt-----atcccat----catta-ctttgaacaaacttt-----------aatttaccagtatctgcaatactccttgtgcag
||||| ||||||||||||||||||||||||||| || ||||||| || ||||| || ||||| |||||||||||||||||||| || |||| |||||||||| || |  || | ||   |  |  |   |  ||||| |     ||   ||    ||||  ||||  ||| | |||           ||| || || ||||||   |  | ||  |||||
AGCAGTGATTTCGATGCGAAGCCAATGGTCATGTTGCTGGGTCAGTATTCCACAGGAAAAACCACATTCATAAAGCATTTACTGAAGACAAATTATCCAGgtaaacaggatgaaatattgtgttccttttccttcttattgagaattatattttccattctctttctacacattttcccttgaaaaaaatgtaacaatatctgagttgtttctcttgcag

upper sequence: GRMZM2G065012_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G46350.2 (Glycine max), 5'ss of exon 9
AGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaataacatggatc---acccat-tgttcttgtatcccatcatt--------actt-tgaacaaac---tttaa-----tttaccagtatc-tgcaatactccttgtgcag-----------------------------------------------------------------------------------
|  || || || ||||| || |||||||| ||||| |||||||| ||||| || || ||||||||||| || || ||| | || ||||  |||||||||||      | |  | |   ||   | |||| | |   | | || |||   |        | || |||| |||    |||||     ||||    | |  |  |||| || ||||  |                                                                                    
AATAGTGACTTTGATGCCAAACCAATGGTTATGCTTTTGGGTCAGTACTCAACTGGTAAAACAACATTTATCAAACATCTGCTTAAAAGTAGTTATCCAGgcacgtgattctcctttctctatatccatatatgtatatgtcacattgcttatatctgatttatgaagaaataattttaaatgcatttatttattttatttaatattctttgtaaaattgtaggatgattaataggatgatataacatatttttaaaatgttattaatctttgtcttgtttttcccataaatgttgatag

upper sequence: GRMZM2G065012_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA18G10150.1 (Glycine max), 5'ss of exon 8
AGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaataacatggatc--acccattgttcttgtatccca-tcattactttgaacaaactttaatttaccagtatctg-caatactccttgtgcag-----
    | || || ||||| || || |||||  |||| |||||||||||||| || |||||||||||||| || |||||| | || ||||  |||||||||||  |   | |  |         |   ||| |  || |||   | | |  |  ||    ||   | |   |    | |  |  | || |   |            
----GTGACTTTGATGCCAAACCTATGGTTTTGCTTTTGGGTCAATACTCAACTGGGAAAACAACATTTATTAAGCATATGCTTAAAAGCAGTTATCCAGGCAAgtgattctcccaaccttgatatattttaattatatgagaatgaccatcttatgtaagaatgagaatggatgaacttaaccattcgattaaaatgaaaggc

upper sequence: GRMZM2G065012_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA17G01310.1 (Glycine max), 5'ss of exon 9
AGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaataacatggatcac-ccatt---gttcttgtatcccatcattacttt------gaacaaactttaatttaccagt-atctgcaat------actccttgtgcag
| ||| ||||| ||||| || ||||||||||||||  | |||||||| ||||| ||||||||||| || ||||| |||||||||| |     ||||||||||     |||    | ||| |    |||     || |  || | |  | ||          | | | |  ||| ||||    | || ||  |       | || |    |||
AACAGTGATTTTGATGCTAAACCAATGGTCATGCTCCTTGGTCAATATTCCACTGGGAAAACAACCTTTATAAAACATTTACTAAGATGTGATTATCCAGgttggttaatt-tgtagataatattatttgaaatccttcatgcaaaaagtatacaatcgagggatataaattactttattgatcatttgtcaccttttaattcttcacacag

upper sequence: GRMZM2G065012_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA07G39450.1 (Glycine max), 5'ss of exon 9
AGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaata---acatggatcacccattgttcttgtatcccatcattactttgaacaaactttaatt------taccagtatctgcaatactccttgtgcag-------------------
| ||| ||||| ||||| || ||||||||||||||  | |||||||| ||||| ||||||||||| |||||||| |||||||||| |     ||||||||||     |||    | ||     |||   ||   || | |   ||||||  |   || |   |   ||       ||| |||  ||  |||  || ||   ||                    
AACAGTGATTTTGATGCTAAACCAATGGTCATGCTCCTTGGTCAATATTCCACAGGGAAAACAACCTTCATAAAACATTTACTAAGATGTGATTATCCAGgttggttaatttttagataatgtaccagatgca-ttatttgaaatcattcatgcaaaaagtataggatcgagggatacaagttactttaatgatcatttgtcaccttttaattcttcacacag

upper sequence: GRMZM2G065012_T03 (Zea mays), 5'ss of exon 9
lower sequence: AT3G20290.2 (Arabidopsis thaliana), 5'ss of exon 9
AGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaataacatggatca--cccattgttcttgtatcccatcattactttgaacaaactttaatttaccagtatctg-caat-actccttgtgcag------------------------------------
| ||| ||||||||||| || || ||||| |||||  |||||||||||||||| || |||||||||||||| |||||||| || ||| | | |||||||||  |   |   |  |    |   |   || | ||| | |  | | | || |||  | |   |  ||  ||   | |   | |||| | |    ||  |                                     
AACAGTGATTTCGATGCAAAACCTATGGTAATGCTTCTGGGTCAATACTCCACAGGAAAAACAACATTCATTAAGCATTTGCTTAAATCTACTTATCCAGgcaagttatccatcttatcctatcttcttctccttctgtgacctaactagtttcgatattttaaaaagtatgggaacaggtcaatgattaaccgtaaaacagctttatataacttcaattgtcatattttttcag

upper sequence: GRMZM2G065012_T03 (Zea mays), 5'ss of exon 9
lower sequence: AT4G05520.1 (Arabidopsis thaliana), 5'ss of exon 9
AGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaataacatggatc-acccattgttcttgtatcccatcattactttgaacaaactttaatttaccagtatctgcaatactccttgtgcag
|| |||||||| ||||| || |||||||| ||||| ||||||||||| ||||| || ||||||||||| ||||| || || ||   |      || |||||| |     |    |   || |  | | |    || |    ||| | | ||  | | | ||    || |||| | ||       ||  |||| |||
AGTAGCGATTTTGATGCCAAACCAATGGTAATGCTTTTGGGTCAATATTCCACCGGAAAAACAACATTTATAAAACACTTGCTCGGATGTGACTACCCAGgtaacttgctttgtttcctctaatcctagcaaatgcaaggaatcttcagtt--atctatctgatcttcaccattgtcc-----tcttgttgt-cag

upper sequence: GRMZM2G065012_T03 (Zea mays), 5'ss of exon 9
lower sequence: Vv19s0090g01130.t01 (Vitis vinifera), 5'ss of exon 9
AGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaataacatggatcacccattgttcttgtat-cccatcattactttgaacaaactttaatttaccagtatctgcaatactccttgtgcag
|  |||||||| ||||| || || ||||| ||||| |||||||||||||| || || ||||| || ||||| || ||||| || || |  |||||||||||||||  | |    |    ||||     | |||||   ||  | |  | ||      | || |  ||||  | | ||| || |     |||  |||
AATAGCGATTTTGATGCCAAACCTATGGTTATGCTTTTGGGTCAATACTCAACTGGAAAAACTACTTTCATTAAACATTTGCTGAAGAGTAGTTATCCAGgtgaattattgttctctcacaccttccctccttgtgcgcctgtgaaaaattc-----agctcttgtttattattttcttcatt-----ttgaacag

upper sequence: GRMZM2G065012_T03 (Zea mays), 5'ss of exon 9
lower sequence: Vv00s0516g00020.t01 (Vitis vinifera), 5'ss of exon 10
AGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaataacatggatcacccattgttcttgtatcccatcattactttgaacaaactttaatttaccagtatctgcaatactccttgtgcag--
   || || || ||||| || || ||||| ||||| |||||||| || || || |||||||| ||||||||||| ||||||||   |   | ||  |||||| |   ||     ||  ||     ||    || |     |  | || ||   |  || ||   ||      |  ||       || || || |   
CATAGTGACTTTGATGCCAAACCCATGGTTATGCTTTTGGGTCAGTATTCAACTGGGAAAACTACATTCATAAAACATTTACTCGGATGTAATTTCCCAGgtaagtaaactttctgtttctgttcttccctttttcagttacaactagttgagaacaatttcgtttcttggcttactatttccttctttttggatag

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|71769027|gb|DR966964.1|DR966964
EST:     CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAG                         GCGCTCATATTGGGCCAGAGCCTACAACGGACAG
genomic: CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaat ... ccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAG
EST: gi|50323441|gb|CO518567.1|CO518567
EST:     CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAG                         GCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT
genomic: CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaat ... ccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT
EST: gi|78124010|gb|DV542394.1|DV542394
EST:     CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAG                         GCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT
genomic: CACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaat ... ccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 145

AGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATCCAGgtgaaacaat ... ccttgtgcagGCGCTCATATTGGGCCAGAGCCTACAACGGACAGGTTTGTTGTCATCACT




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