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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagtttatactgcttctgttcgagctttccttccctgttggtgtcctcactgacaacaattaactctgaaatctacatcaaag

Basic information

species Zea mays
transcript GRMZM2G077299_T03
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077299_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 5'ss of exon 8
GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagtttatactgcttctgttcgagctttccttccctgttggtgtcctcactgacaacaattaactctgaaatctacatcaaag-----------------------------
||| |||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| | ||||||     | |   | |   ||||| ||  ||  |   ||||| |    ||   |||  || |||  |||| ||                                  
GAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAATTTCTCCAGgtactagtttacttgacattattcctgcctttcattttcttatcacgtcctaat---catatattgcctttgagttctatatttttctaatgaaaactttgaactccacatcaaag

upper sequence: GRMZM2G077299_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 8
GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagttta-----tactgcttctgttcgagctttcctt------ccctgttggtgtcct--cactgacaacaatt---------------aactctgaaatctacatcaaag
||| |||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| ||||| ||||| ||||||||      | |  ||| |  |    ||| |||      ||||  |  | |  |  |  |||   | |||               || | |||| ||||||||||||
GAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAGTTTCTCCAGgtaccagtttagttgacattatttccgcccttcattttcttatcactccctaatcatatattgcctttgaattctatttttttttctaatgaaaaatttgaactctacatcaaag

upper sequence: GRMZM2G077299_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA03G27490.1 (Glycine max), 5'ss of exon 7
GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgt--gccagtttatactgcttctgttcgagctttccttccctgttggtgtcctcactgacaacaattaactctgaaatctacatcaaag
|| |||   | |||| || ||||||||||||||||| ||||| || |||||||||  ||| ||||| ||||| ||  |||| || | |||   |||||| ||  | |  |||||  || |     ||   | ||   |   | |||      ||| | | || ||   | | |    | |   |     
GAAAGATAGTGTTGGACCCTGGGAAGAGAGACCTGGTCACTTTGGTGATGTTTGGAGTTATTGGACAGATGAAGGATTTGGTTATTTTGAGGGTCTTCAAgtaagtccatttattatgataacaatca--cattttgttgttattgtgaaattcaatcataataagccattttttg-tgtgtgtag---

upper sequence: GRMZM2G077299_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA19G30450.1 (Glycine max), 5'ss of exon 8
GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagtttatactgcttctgttcgagctttccttccc--tgttggtgtcctcactgacaacaattaactctgaaatctacatcaaag----------------------------------
|| |  ||| ||||| |||||||| ||||||||||| ||||| || |||||||||   ||||||||||||||||| ||||| || ||||| ||||| || ||    |  | |  | | | | ||  |||||    |     |||| || ||    |  |  ||   ||  | ||  ||     | |||                                   
GAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTGGATGTACTGGACTGATGATGGACTTGGTTATTATGAGTTTCTCCAAgtaagtgcctct-ttacatatattgtagcttaggattatgatgttcgtatctagtcgaattact-ctagttgtgctatgctagtgaaatgatatatataattattattataatttttgagcag

upper sequence: GRMZM2G077299_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA03G00630.1 (Glycine max), 5'ss of exon 7
GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagtttatactgcttctgttcgagctttccttccctgttggtgtc-ctcactga--caacaattaactctgaaatctacatcaaag--
|| |||  |  |||| ||||||||||||||||| |||||||  || ||||| ||| |||| |||| |||||| ||  |||| | || |||    ||||| ||     ||  |  |   |    ||  || |   |      ||  | |  || | |||    | || |   ||| |  | |   || |    
GAAAGACACAGTTGGACCATGGGAAGAGAGACCAGGACACTATGGAGATGTATGGAATTATTGGAGTGATGACGGATTTGGTTTCTTTGAGGGCCTTCAAgtagggtttcctttta--taaactcatgcatatatggatatttaatttttcttattgaattgagaaatcgatct-atttgtttctcgagcag

upper sequence: GRMZM2G077299_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA03G27460.3 (Glycine max), 5'ss of exon 8
GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgt----gccagtttatactgcttctgttcgag--------ctttccttccctgttgg--tgtcctcactgacaacaat--taactctgaaatctacatcaaag--------------------
|| || |||| |||| |||||||| ||||||||||| ||||| || |||||||||   ||||||||||||||||| ||||| || ||||| ||||| || ||    |||  |||  |    || |    |||          ||| |  |  ||||   |   ||   |     | ||  ||        || || || |                       
GAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTGGATGTACTGGACTGATGATGGACTTGGCTATTATGAGTTTCTCCAAgtaagtgcctcttttcatatattgtagctgaggaatatgatgttcatatctagttgaattactcttgttttgtgctatgctagtgaaatgatatatattattattattattatttttgagcag

upper sequence: GRMZM2G077299_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA19G30460.1 (Glycine max), 5'ss of exon 7
GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagtttatactgcttctgttcgagctttccttccctgttggtgtcctcactgacaacaattaactctgaaatctacatcaaag
|| |||  ||||||| |||||||| ||||||||||| ||| | || ||||||||| | || |||| |||||||||  |||| |  | ||| | ||| | ||||  |||         |||| ||  | || |  ||   | |||   | || | | |  | |||    | | | || |       ||
GAAAGATACTATTGGACCATGGGAGGAGAGACCTGGGCACCTTGGTGATGTTTGGAACTATTGGAGTGATGATGGAATTGGTTTTTTTGAGTATCTCCTGgtg--agt--------attcttttacaactataattaaat-ttgtcctgctgaataaatataatatgatttaatatttcttgagcag

upper sequence: GRMZM2G077299_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagtttatactgcttctgttcgagctttccttccctgttggtgtcctcactgacaacaattaactctgaaatctacatcaaag
|| |||| |  |  |  | ||||||||||||||||| || |  || ||||||||| | |||||||||||||||||||||||  ||| ||||||  |||| ||    | || |  |  ||  | |      | | ||    ||  || ||   | | || |   |  |  |  | || |     |   
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagggatttttttcttttcggttctatatccatttaaagt--gtttcaataattactaagctcgaaacaaatatttcttgtag--

upper sequence: GRMZM2G077299_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 5'ss of exon 8
GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagtttatactgcttctgttcgagctttccttccctgttggtgtcctcactgacaacaattaactctgaaatctacatcaaag---
|| |||| |  | || || |||||||||||||| || || || || ||||||||| | || ||||| ||||||||||||||  ||| ||| ||  |||| |||       | ||| ||||| ||| |   ||   | | |  || |  || |   |      ||| | | | ||||  ||||    |   
GAAAGAAACCGTAGGACCTTGGGAAGAGAGACCGGGCCATTTTGGTGATGTTTGGAAGTATTGGACCGATGATGGCCTTGGCCACTTTGAGTTCTTTCAAgtg-------agacttcttcttttcta---ttgagtacataatgat--ccccgaagctcgttattgaatattaaatgaacattcttgcag

upper sequence: GRMZM2G077299_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 5'ss of exon 9
GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgc-cagtttatactgctt--ctgttcgagctttccttc----cctgttggtgtcctcactgacaacaattaactctgaaatctacatcaaag---------------
|| | |  | ||||| || ||||| ||||||||||||||||| || ||||||||| | ||||||||||||||||| ||||| || | ||| || ||||| ||    |  ||  ||   |    |||   || |||  ||     | |  || |      | |  ||  |  |    || |  |      ||||                
GAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTGGAAGTACTGGACTGATGATGGACTTGGTTATTTTGAGTTCCTTCAAgtatgtatcttccacctgtcaattgtgaaagattttatttatatcttagtgattgtacaatttccatgagatgctgcttaggtaatttacaaatgttttgtttctgtag

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|12045517|gb|BF727656.1|BF727656
EST:     GAATTTCTTCAG                         CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG
genomic: GAATTTCTTCAGgtgccagttt ... tacatcaaagCTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG
EST: gi|6095297|gb|AW119964.1|AW119964
EST:     ATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAG                         CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG
genomic: ATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagttt ... tacatcaaagCTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG
EST: gi|211082959|gb|FL420012.1|FL420012
EST:     TTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTNTTCAG                         CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagttt ... tacatcaaagCTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG
EST: gi|78179997|gb|DV550370.1|DV550370
EST:     TTTGGAATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAG                         CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagttt ... tacatcaaagCTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG
EST: gi|211043015|gb|FL421679.1|FL421679
EST:     TTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAG                         CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagttt ... tacatcaaagCTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG
EST: gi|71441725|gb|DR822775.1|DR822775
EST:     TTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAG                         CTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagttt ... tacatcaaagCTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG

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: 47 (upstream exon), 49 (downstream exon)
Score: 54

GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagttt ... tacatcaaagCTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagttt ... tacatcaaagCTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 56

GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagttt ... tacatcaaagCTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 915

GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagttt ... tacatcaaagCTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG