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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcctctttctctgtatggctaatagtcaacttgaaataagactataagagagtcctcaaatggtgacttactgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT

Basic information

species Zea mays
transcript GRMZM2G143356_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 4
gtatgcctctttctctgtatggctaatagtcaacttgaaataagactataagagagtcct--caaatggtgacttactg----aactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
|||||| | ||| | | ||||  | |||  | | |  |||   ||  |  || ||    |  || |   |  |||         | ||||||||| || ||||| |||||||| || ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| || || ||| |
gtatgcatttttatttttatgatttataacctattacaaaatggagaaccagtgaacaataacagacattttcttttaataccgattgcagTTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTTCAACAATCATT

upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
gtatgcctctttctctgtatggctaatagtcaacttgaaataagactataagagagtcctcaaatggtgacttactgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
|||| |||||||   |       |  |  | |       ||     | | |       | |   || ||  ||      |||||||||| || || || ||||| || ||||| ||||||||||||||||| ||  |||| ||||| |||||||     |||||  | || || ||||| || ||
gtatccctcttttatttccctttttctcttaaggcccgtatcctcttttcaa----ctcactcgtgttgcttt------ctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT

upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S245_10V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------gtatgcctctttctctg-----tatggctaatagtcaacttgaaataagactataagagagtcctc-----aaatggtgacttactgaac-----tgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
                                                | || |||     ||||      ||   |    |  |||   | ||    ||     ||    |||     |||  || || |     ||     ||||||||| || || |||||||| || ||||||||||||||||||||||| |||   ||    ||  ||   ||    ||||| ||||| || |||   |||||
gtatttgctgacgctaaaccctcgcagcattgtgaagcatgttcgatcgaataccttgcaatctgagcttcattcttgtaggaaaacaaaacattttgctgatctagttctctcttgctaaaaagtaacctttgtgacctttgtgcagTTGGAGGTCTCCTGAATGCAACTTTTGGAAATGCAACTGAAATGATTATTTGTATCATGGCCCTGCGGAAGAATATGATACGAGTTGTACAGTTATCACT

upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S79_95V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------gtatgcctctttctctgtatg-gctaatagtcaacttgaaataagacta--taagagagtcctcaaatggtga-------cttactgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
                                            || ||| | | |  |  | || |||       |     || |  |  |   | |   | | |||  | |  ||       |||    |  ||||||||| || || |||||||| || |||||||||||||||||| |||| |||    |    ||| |    ||    ||||| ||||| || ||    |||||
gtgattgccgaagttcgaatgttgctgccttatgaagcatattggtttgcatttcttgcaatctgtgctgcagaataggggcaagtgtgtttggctgattcaattctctgacgaagaaactgatctttgctatttgcagTTGGAGGTCTCCTGAATGCGACCTTTGGAAATGCAACTGAAGTGATTATTTGTGTCATGGCTCTCCGGAAGAACATGATACGAGTTGTACAATTATCACT

upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
----gtatgcctctttctctgtatggctaatagtcaacttgaaataagactataagagagtcctc----------aaatggtgacttactgaact-gcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCAT-TGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
     || |    |  |     ||||      |     ||||  |||  ||   |       |||          |||   ||  ||  |  ||| |||||||| || ||||||||||| || ||||| |||||||| |||||||| || ||||  || ||||||    ||   |||||| ||||| || |||   |||||
taatttaagttgttaacgggtaatgggagggtggttgattgatctaaagctcctatctctctctctctctcggctaaagaatggtttttttcacttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCAT-TGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT

upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ12361 (Selaginella moellendorffii), 3'ss of exon 1
gtatgcctctttctctgta-tggctaatagtcaacttgaaataagactataagagagtcctcaaatggtgacttactgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
                ||| |   | |||  |   |    || | |     || || |  ||   |  ||  |  ||    |||||| ||||||||||||||||| || ||||||||||| || || ||||| ||  | || |  ||| ||   ||||| |||||||| || || |||| ||| ||
----------------gtaataaattatacccttttctcgatcacaaagagagtgaatggtcctttt-tgtttctct----tgcagTCGGTGGCCTTCTGAATGCGACGTTTGGAAATGCCACCGAGATGATTATCTCTATCTTCGCTCTGCGGAATGGCATGATCCGCGTGGTTCAGCTGTCGCT

upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ33760 (Selaginella moellendorffii), 3'ss of exon 1
gtatgcctctttctctgta-tggctaatagtcaacttgaaataagactataagagagtcctcaaatggtgacttactgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
                ||| |   | |||  |   |    || | |     || || |  ||   |  ||  |  ||    |||||| ||||||||||||||||| || ||||||||||| || || ||||| ||  | || |  ||| ||   ||||| |||||||| || || |||| ||| ||
----------------gtaataaattatacccttttctcgatcacaaagagagtgaatggtcttttt-tgtttctct----tgcagTCGGTGGCCTTCTGAATGCGACGTTTGGAAATGCCACCGAGATGATTATCTCTATCTTCGCTCTGCGGAATGGCATGATCCGCGTGGTTCAGCTGTCGCT

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|148951918|gb|EC897694.2|EC897694
EST:     GCAGCTTGCAGTATACACTGGTCCAACAG                         TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG
EST: gi|211103676|gb|FL335622.1|FL335622
EST:     GCAGCTTGCAGTATACACTGGTCCCACAG                         G
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcag-
EST: gi|211103676|gb|FL335622.1|FL335622
EST:     GCAGCTTGCAGTATACACTGGTCCCACAG                         G
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcag-
EST: gi|211203502|gb|FL354146.1|FL354146
EST:     GCAGCTTGCAGTATACACTGGTCCAACAG                         TTGGTGGCCTTCTGAATGCTAACATT-GGAAAATGCA-CTGGAATGATCAT
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTA-CATTTGGAAA-TGCAACTGAAATGATCAT
EST: gi|148952030|gb|EC897816.2|EC897816
EST:     GCAGCTTGCAGTATACACTGGTCCAACAG                         TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG
EST: gi|149080754|gb|EE169818.2|EE169818
EST:     GCAGCTTGCAGTATACACTGGTCCAACAG                         TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG
EST: gi|211019237|gb|FL365611.1|FL365611
EST:     GCAGCTTGCAGTATACACTGGTCCCACAG                         TTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATT
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTT-GGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATT
EST: gi|149075868|gb|EE164419.2|EE164419
EST:     GCAGCTTGCAGTATACACTGGTCCAACAG                         TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG

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: 32 (upstream exon), 49 (downstream exon)
Score: 66

GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT


Block sizes: 29 (upstream exon), 47 (downstream exon)
Score: 119

GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 112

GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT


Block sizes: 29 (upstream exon), 49 (downstream exon)
Score: 124

GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacttgaaataagactataagagagtcctcaaatggtgacttactgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
                                      gacttac  putative branch site (score: 124)
       aaataagactataa  TA-rich tract