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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcaatgacacccacttgagttttcttttgtataatgtattatgcatgtttttatacaaactccttttttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGGTGCAACAAATTATGGAATGCCATCCGTTTTGCGATGGGCAAACTGGGTG

Basic information

species Zea mays
transcript GRMZM2G117870_T02
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117870_T02 (Zea mays), 3'ss of exon 17
lower sequence: PP1S84_125V6.1 (Physcomitrella patens), 3'ss of exon 16
-------------gttcaat-gacacccacttg---agttttcttttgtataa-tgtattatgcatgttt--ttatac--aaactccttttttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGGTGCAACAAATTATGGAATGCCATCCGTTTTGCGATGGGCAAACTGGGTG
              || |||  |    ||||||   | | |   | |   ||| | |     |  |||||  |||| |         | |  |  ||||| | |  |  |||||||||||||||    | ||||| |||||| | ||||||||||||||| | ||||||| ||| |||||||| |||   || || ||| 
catttgtttatcaattaaattaatcttcacttggtgaatatctgtatacgtaaatattccgaggttgtttacttatgcttgggtggatctcattgttcagGCGGTGAATATAAATCTTGATATTCTTCGTGTGGTGGGATACCGCCAGTGGTGCAACAAACTTTGGAATGTCATTCGTTTTGCCATGACGAACCTTGGTA

upper sequence: GRMZM2G117870_T02 (Zea mays), 3'ss of exon 17
lower sequence: EFJ27321 (Selaginella moellendorffii), 3'ss of exon 13
gttcaatgacacccacttgagttttcttttgtataatgtattatgcatgtttttatacaaactccttttttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGGTGCAACAAATTATGGAATGCCATCCGTTTTGCGATGGGCAAACTGGGTG
                  |||||   || |    |  |      | | |||| || ||   || |  |||     ||||| || |  || ||| | ||  |  || | |||| ||| |||||| | |||||||||||| | |||||||| ||||| |||||||||   || |||||||
--------------gtacgagttcaattcttcccacagg-----ggaagtttctaaactc-cttccatttgtgcgcagTCCGAGAACATCAATTTGGACGTCCAGCGTGTGGCTGGCTACAGATACTGGTGCAACAAACTCTGGAATGCAATCCGATTTGCGATGCTGAACCTGGGTG

upper sequence: GRMZM2G117870_T02 (Zea mays), 3'ss of exon 17
lower sequence: EFJ35310 (Selaginella moellendorffii), 3'ss of exon 13
gttcaatgacacccacttgagttttcttttgtataatgtattatgcatgtttttatacaaactccttttttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGGTGCAACAAATTATGGAATGCCATCCGTTTTGCGATGGGCAAACTGGGTG
                  |||||   || |    |  |      | | |||| || ||   || |  |||   | ||||| || |  || ||| | ||| |  || | |||| ||| |||||| | |||||||||||| | |||||||| ||||| |||||||||   || |||||||
--------------gtacgagttcaattcttcccacaggg----gaaagtttctaaactc-cttccatttgtgtgcagTCCGAGAACATCAATTTGGATGTCCAGCGTGTGGCTGGCTACAGATACTGGTGCAACAAACTCTGGAATGCAATCCGATTTGCGATGCTGAACCTGGGTG

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|211262428|gb|FK977273.1|FK977273
EST:     AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAG                         TCTGACAGGATAAATCYTGATATTAAGAAGGTGGTTGGATACAGACAGTGG
genomic: AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAGgttcaatgac ... tttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
EST: gi|26456963|gb|CA828546.1|CA828546
EST:     ATGTGGTACCGATGCTCTACGCTTTGGCACTGATATCGTACACTTCCCAG                         TCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
genomic: ATGTGGTACCGATGCTCTACGCTTT-GCACTGATATCGTACACTTCCCAGgttcaatgac ... tttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
EST: gi|211262422|gb|FK977267.1|FK977267
EST:     AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAG                         TCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
genomic: AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAGgttcaatgac ... tttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
EST: gi|67010640|gb|CO439389.1|CO439389
EST:     AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAG                         TCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
genomic: AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAGgttcaatgac ... tttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
EST: gi|211259993|gb|FK977263.1|FK977263
EST:     AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAG                         TCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
genomic: AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAGgttcaatgac ... tttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
EST: gi|31364366|gb|CD448721.1|CD448721
EST:     AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAG                         TCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
genomic: AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAGgttcaatgac ... tttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
EST: gi|211262427|gb|FK977272.1|FK977272
EST:     AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAG                         TCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
genomic: AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAGgttcaatgac ... tttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
EST: gi|71421135|gb|DR805313.1|DR805313
EST:     AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAG                         TCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
genomic: AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAGgttcaatgac ... tttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
EST: gi|50330120|gb|CO525246.1|CO525246
EST:     AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAG                         TCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG
genomic: AATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAGgttcaatgac ... tttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGG

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: 279

AAACATTGCAAGAGATGGGAAGAAGAAGGATTTTCCTGATGGCATAGCAGAATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAGgttcaatgac ... tttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGGTGCAACAAATTATGGAATGCCATCCGTTTTGCGATGGGCAAACTGGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

AAACATTGCAAGAGATGGGAAGAAGAAGGATTTTCCTGATGGCATAGCAGAATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAGgttcaatgac ... tttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGGTGCAACAAATTATGGAATGCCATCCGTTTTGCGATGGGCAAACTGGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

AAACATTGCAAGAGATGGGAAGAAGAAGGATTTTCCTGATGGCATAGCAGAATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAGgttcaatgac ... tttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGGTGCAACAAATTATGGAATGCCATCCGTTTTGCGATGGGCAAACTGGGTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 251

AAACATTGCAAGAGATGGGAAGAAGAAGGATTTTCCTGATGGCATAGCAGAATGTGGTACCGATGCTCTACGCTTTGCACTGATATCGTACACTTCCCAGgttcaatgac ... tttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGGTGCAACAAATTATGGAATGCCATCCGTTTTGCGATGGGCAAACTGGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttttgtataatgtattatgcatgtttttatacaaactccttttttcattcagTCTGACAGGATAAATCTTGATATTAAGAGGGTGGTTGGATACAGACAGTGGTGCAACAAATTATGGAATGCCATCCGTTTTGCGATGGGCAAACTGGGTG
                                      ctccttttttcattc  CT-rich tract
     ttgtataatgtattat  TA-rich tract