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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCGCAGCAGCCTCATTTGAGCATTCCAGAGACTGAAACTGGAAAAGCACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgcatgcacccttgagtttgtgaatggttgaattaacatcatactgaacatagaactataagagtacaggtgcaatgattagaaatctatctgtctgctgatgctaatatataatagtccttaaatattcagtcaatgtgaaagttctatgaggtctgacttatgctgatactgcactaataatttgcag

Basic information

species Zea mays
transcript GRMZM2G004459_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004459_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g59590.1 (Oryza sativa), 5'ss of exon 13
GCTGCGCAGCAGCCTCATTTGAGCATTCCAGAGACTGAAACTGGAAAAGCACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtga-gttgcatgcacccttgagtttgtgaatggttgaattaacatcatactgaacatagaactataagagtacaggtgcaatgattagaaatctatctgtctgctgatgctaatatataatagtccttaaatattcagtcaatgtgaaagttctatgaggtctgacttatgctgatactgcactaataatttgcag
|||||||||||||||||| |||||||||||||||||||| |||| ||| ||||  | ||||| || |||||||| |||||||| || ||||||||||| ||| | |     | ||| || ||   |     ||  |  | |  | ||  | | |        || | | | | ||  || | ||  || |||| |||   |||    || |||                                                                                    
GCTGCGCAGCAGCCTCATCTGAGCATTCCAGAGACTGAAGCTGGGAAAACACGCAGACAATACCGTCAACTTCTGAACCGTTCCCTTATGGTTGTCTCAGgtaaagccagttccacactcgacagtcctgttgtgtttactctcgtcgcatttac------gctcttatactgcat-tgtattg--tacaaatatat---tctataaat-cta------------------------------------------------------------------------------------

upper sequence: GRMZM2G004459_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g62570.1 (Oryza sativa), 5'ss of exon 14
GCTGCGCAGCAGCCTCATTTGAGCATTCCAGAGACTGAAACTGGAAAAGCACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgcatgcacccttgagtttgtgaatggttgaattaacatcatactgaacatagaactataagagtacaggtgcaatgattagaaatctatctgtctgctgatgctaatatataatagtccttaaatattcagtcaatgtgaaagttctatgaggtctgacttatgctgatactgcactaataatttgcag
|| ||||||||||||||||||||||| |||||||||||| |||| ||| |||   ||||||| || |||||||| |||||||| || | ||||||||| ||| ||||     ||  |||  |  | | ||  || |  |    ||    ||  |         | ||    |      |||| | || | |    |  |                                                                                                 
GCGGCGCAGCAGCCTCATTTGAGCATCCCAGAGACTGAAGCTGGGAAAACACACAGGCAATACCGTCAACTTCTGAACCGTTCCCTCACGGTTGTCTCAGgtaagttagtgtcaagcttctgcctctaaagtgt-gtttctgtatttgcctttatgctctggcacaaatcgatcatgccaattactacagaatagtaagag-----------------------------------------------------------------------------------------------
















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|6601653|gb|AW256049.1|AW256049
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|60397275|gb|DN230091.1|DN230091
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|60343446|gb|DN210419.1|DN210419
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|60347607|gb|DN214580.1|DN214580
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|211170842|gb|FL475250.1|FL475250
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|211263258|gb|FL469989.1|FL469989
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|94472827|gb|EB701785.1|EB701785
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|60399644|gb|DN232454.1|DN232454
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|6526638|gb|AW215933.1|AW215933
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|31362359|gb|CD446716.1|CD446716
EST:     ACGTCGGCAATATCGACAACTTCTAAACCGTTCTCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|60356872|gb|DN223845.1|DN223845
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|7162467|gb|AW520089.1|AW520089
EST:     ACGTCGGCAATATCGACAACTTCTAAACCGTTCTCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|6022207|gb|AW067135.1|AW067135
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|31351610|gb|CD435967.1|CD435967
EST:     ACGTCGGCAATATCGACAACTTCTAAACCGTTCTCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|32840503|gb|CD980184.1|CD980184
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGTTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|32840530|gb|CD980211.1|CD980211
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGTTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|60337295|gb|DN204268.1|DN204268
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|32840487|gb|CD980168.1|CD980168
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGTTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|24765757|gb|CA400916.1|CA400916
EST:     ACGTCGGCAATATCGACAACTTCTAAACCGTTCTCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|83279244|gb|DV943252.1|DV943252
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|78084948|gb|DV513341.1|DV513341
EST:     ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|60353128|gb|DN220101.1|DN220101
EST:     ACGTCGGCAATATCGACAACTTCTAAACCGTTCTCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
EST: gi|31352762|gb|CD437119.1|CD437119
EST:     ACGTCGGCAATATCGACAACTTCTAAACCGTTCTCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG
genomic: ACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAG

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: 171

GCTGCGCAGCAGCCTCATTTGAGCATTCCAGAGACTGAAACTGGAAAAGCACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAGCTCGGAAGAACTCGTCCTCTTGAAGCCTCCCCTACTGGACAATTGGGGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 70

GCTGCGCAGCAGCCTCATTTGAGCATTCCAGAGACTGAAACTGGAAAAGCACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAGCTCGGAAGAACTCGTCCTCTTGAAGCCTCCCCTACTGGACAATTGGGGA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 51

GCTGCGCAGCAGCCTCATTTGAGCATTCCAGAGACTGAAACTGGAAAAGCACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAGCTCGGAAGAACTCGTCCTCTTGAAGCCTCCCCTACTGGACAATTGGGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

GCTGCGCAGCAGCCTCATTTGAGCATTCCAGAGACTGAAACTGGAAAAGCACGTCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgca ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGATTAGCTGCTTATCGGGTTTATGCAGCTCGGAAGAACTCGTCCTCTTGAAGCCTCCCCTACTGGACAATTGGGGA