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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgctttcagatttctcttacacgtcatttacgaattgctcatgtagtcatgttatgctgcggccagcttcacacatattggttgcccatttcatgagtatctcaatcacatttcacattgtacccgaacttgattaccgaatttacataaaaaaccctttcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG

Basic information

species Zea mays
transcript GRMZM2G002859_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002859_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os10g36870.1 (Oryza sativa), 3'ss of exon 9
gtagtgctttcagatttctcttacacgtcatttacgaattgctcatgtagtcatgttatgctgcggccagcttcacac-atattggttgcccatttcatgagtatctcaatcacatttcacattgtacccgaacttgattac--cgaatttacataaaaaaccctttcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG
                                                          | | ||  | | |||| ||    |   ||| |  |    |    |||||       | ||    ||||   | || |||  |||    || ||   |  |  | |||   | ||||||||||| |||||||||||||| |||||||||||||| ||||||||||| |||||||| |||||||||||||||||| |||| |||||||||||||||||||
---------------------------------------------------------gtacggcc-ctatcttcccattggacatgtttctaaccataaacatatctttgctggactt----ttgtgggcaaagttggctacactaaacttgtgttcattaacctgctc-aatcagGTGTCAAACAATGGATGGGCAGAAGGTGAATGCAGAGGGAAAGCTGGCTGGTTCCCTTACGACTACATCGAGAAAAGGGACCGTGTGCTTGCAAGTAAAG

upper sequence: GRMZM2G002859_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G01100.2 (Glycine max), 3'ss of exon 9
gtagtgctttcagatttctcttacacgtcatttacgaattgctcatgtagtcatgttatgctgcggccagcttcacacatattggttgcccatttcatgagtatctcaatcacatttcacattgtacccgaacttgattaccgaatttacata------aaaaaccctttcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG
                                                                           || || |        | |||  |     |   | |     |  | |    |||| ||  | |||||  | |||| ||       || |   || |  |   |||||| | |||||||||||||| || ||||||||||  |||||||| |||||||| || |  |  ||||| || | | ||||||| || || ||||| || |
---------------------------------------------------------------------------catatttaaaacaaacttttggttgtggtggtagtggggatggata----accctaaaatcattacatattttaaattgttcccaatatgactctgattggcagGTGACAAACAATGGATGGGCTGAGGGTGAATGCAAAGGGAAAGCAGGTTGGTTTCCATTTGGTTACATTGAAAGAAGGGAGCGAGTCCTCGCAAGCAAGG

upper sequence: GRMZM2G002859_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 9
gtagtgctttcagatttctcttacacgtcatttacgaattgctcatgtagtcatgttatgctgcggccagcttcacacatattggttgcccatttcatgagtatctcaatcacatttcacattgtacccgaacttgattaccgaatttacataaaaaaccctttcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG
                                                    |    |  ||       | |      ||| |||   |  ||| | | |  |||   | || |||  | ||||| ||| ||  ||| |  |  ||| |  | | |              |||||| | |||||||||||||| || ||||||||||  |||||||| |||||||| || |  |  ||||| || | | ||||||| || || ||||| || |
----------------------------------------------------aaaacaaacttt---tggttgtggtgatagtgggaacggattaccttaaaatcatta-catattctaaattgttccc-aatatgact--ctgattgaattgaca--------------cagGTGACAAACAATGGATGGGCTGAGGGTGAATGCAAAGGGAAAGCAGGTTGGTTTCCATTTGGTTACATAGAAAGAAGGGAGCGAGTCCTCGCAAGCAAGG

upper sequence: GRMZM2G002859_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 9
gtagtgctttcagatttctcttacacgtcatttacgaattgctcatgtagtcatgttatgctgcggccagcttcacacatattggttgcccatttcatgagtatctcaatcacatttcacattgtacccgaacttgattaccgaatttacataaaaaaccctt-----tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG
                                                      |||     |    |    || |||||        || |     |     | | | ||| |||   || |         |   | |      || | |||  |   |  |     || |   |||||  |   || |||||||||||||||||||||||  || ||||||||||||||||| || |  ||||| || | |||||| || || ||||| || ||||
------------------------------------------------------gttcgatagtaaaccaactcccacatgagaaaaaccaacaaagtctcc-tttaattcatattaaccaatacggttattcagtagtgtttgtttgatataccacttctctatttgtcattgccagGTTACAGGCAGTGGATGGGCCGAAGGTGAATGCAAAGGCAAAGCTGGTTGGTTCCCTTATGGGTACATTGAAAGACGGGAACGAGTTCTTGCTAGCAAAG

upper sequence: GRMZM2G002859_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 9
gtagtgctttcagatttctcttacacgtcatttacgaattgctcatgtagtca-tgttatgctgcggccagcttcacacata-ttggttgcccatttcatgagtatctcaatcacatttcacattgtacccgaacttgattaccgaatttacataaaaaaccctttcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG
                                                  ||| ||||  ||||   |||  |   ||||   ||| ||| |  ||| ||   ||| |  | ||         |||||   |   || ||     | |||| ||           |  |  | ||||||| || ||||||||||| |||||||||||||  || || || ||||||||||| |  |  ||  | || || ||||| || || |||||||| ||  
------------------------------------------------cttcactgttcagctgaaaccaa-tgggcacacggttgtttgtcttttttatt--tatttggacca-------tgttgtaatagcgtttcat-----actttatat-----------ttttggt-agGTGTCTAATAATGGATGGGCTGAAGGTGAATGCAAAGGAAAGGCAGGTTGGTTCCCATTTGGATATGTTGAAAAGCGGGAACGGGTTCTTGCAAGCAAGA

upper sequence: GRMZM2G002859_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 9
gtagtgctttcagatttctcttacacgtcatttacgaattgctcatgtagtcatgttatgctgcggccagcttcacacatattggttgcccatttcatgagtatctcaatcacatttcacattgtacccgaacttgattaccgaatttacataaaaaaccctttcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG
                                                                   |   ||  ||  |||   ||||  |||    |  | | |  ||    ||  |  || || || |  |   ||||   || |    |       || | ||   |||||||| |||| ||| ||||| |||||||||||||| || ||||| |||||||||||    |  ||||| || | ||| || || || |||||||| ||  
-------------------------------------------------------------------cctttttgca-gtatatcttgcttattcttagcatgtttggatttggtt--atcttttatcccagttcttttacgagatctgttcac---tttctgtgcttggcagGTGTCAAACAGTGGCTGGGCAGAAGGTGAATGCAGAGGAAAAGCAGGTTGGTTCCCAGTTGGATACATAGAAAGACGAGAACGCGTTCTTGCAAGCAAGT

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|71307047|gb|DR789678.1|DR789678
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|149070323|gb|EE158722.2|EE158722
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGGACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|33091909|gb|CF051903.1|CF051903
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|148986436|gb|EE030178.2|EE030178
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|40336986|gb|CK371056.1|CK371056
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|40335185|gb|CK369255.1|CK369255
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|101396723|gb|EB820287.1|EB820287
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|60356623|gb|DN223596.1|DN223596
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|211534621|gb|FL443302.1|FL443302
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|37385184|gb|CF629716.1|CF629716
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|37380473|gb|CF627052.1|CF627052
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
EST: gi|38687511|gb|CK144542.1|CK144542
EST:     GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG
genomic: GCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGG

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: 49 (upstream exon), 49 (downstream exon)
Score: 159

GCAATCCAGTCATACCAAGCCGAAAGCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 98

GCAATCCAGTCATACCAAGCCGAAAGCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 94

GCAATCCAGTCATACCAAGCCGAAAGCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 68

GCAATCCAGTCATACCAAGCCGAAAGCGATACCGAGCTCAACCTTTCAACTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattgtacccgaacttgattaccgaatttacataaaaaaccctttcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAAAGCTGGTTGGTTCCCCTACGACTACATCGAGAAACGGGAGCGTGTGCTTGCAAGTAAAG
             acttgat  putative branch site (score: 68)
                                        ccctttcct  putative PPT
                         aatttacataaaaaa  TA-rich tract