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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTATCTCCTGGTCTGTCACCATGGTTCAGCGATTAACGTACCGTCGCCGCCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgccttccctctctctttgtcgcgaattttctaggctacggatttcggcttagatatttcggcatcgtgttttggggtttggggccagcattgt...

Basic information

species Physcomitrella patens
transcript PP1S200_25V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S200_25V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os08g33920.1 (Oryza sativa), 5'ss of exon 1
GCTATCTCCTGGTCTGTCACCATGGTTCAGCGATTAACGTACCGTCGCCGCCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgccttccctctctctttgtcgcgaattttctaggctacggatttcggct-tagatatttcggcatcgtgttttggggtttggggcc-agcattgt-----
     |  | |   || |   ||||| |||||  | || |||||    || ||| |||| || || ||||||||||||||| | || |||||||||||||||||   |  | |  |||  |||      ||||||||| |    | | | | |  | | ||| | | |      |||  || | || | ||   |   ||||     
CGCGGCGGCGGCGGTGGCGAGATGGTGCAGCGGCTCACCTACCGGAAGCGTCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAGgtac---ggatccgttcttgcttgaa---gaattttcttgttgcctggtgtggtttcttgatctgttgcagatttgtgatgtgtttggtggtggattgttgttgcag

upper sequence: PP1S200_25V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G175882_T01 (Zea mays), 5'ss of exon 1
GCTATCTCCTGGTCTGTCACCATGGTTCAGCGATTAACGTACCGTCGCCGCCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacact--gc-cttccctctctctttgtcgcgaattttctaggctacggatttcggctta-----gatatttcggcatcgtgttttggggtt---tggggccagcattgt-----------------------------------------------------------------------------------------
| |    |    |  | ||  ||||| | | |  | || |||||    || ||| |||| |||||||| ||||||||||||||||| |||||||| || ||||   |  || |   | || | | ||||  |   |  |  ||| |   ||  | || ||      ||| | |     |  || || || |||   |||  |   | |||                                                                                          
GATGGTGCGGCTTGGGGCAAGATGGTGCGGTGGCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcagcgcactcatcccgcgttgtttctgttcgtgcaggttgtagagataggattctcgctgatttgttcatgttttggttaggagttagatggatctgcccttgagatctaggaccctttagaccggatatcgcaccgttaccacttaatctcgtatattcacttagtgtcgttgttgtgatgtagttgattag

upper sequence: PP1S200_25V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G152573_T04 (Zea mays), 5'ss of exon 1
--GCTATCTCCTGGTCTGTCACCATGGTTCAGCGATTAACGTACCGTCGCCGCCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgta----cactgccttccctctctctttgtcgcgaattttctaggc-tacggatttcggcttagatatttcggcatcgtgttttggggtttggggccagcattgt
     | |  ||||     ||  ||||| |||||  | || |||||    || ||| |||| |||||||| ||||||||||||||||| |||||||| || ||||    ||  ||  || ||   ||  |  | ||   |||||   | | | | ||   |       |||   || |  | | ||   |||| ||    |      
GAAGCAGCGGCTGGG--AGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcagcgcactcgcttggtcgatcccacgttgtttctgttcgtgcaggttgtagagataggattctcgc-tgatttgttcatgttttggttaggag----

upper sequence: PP1S200_25V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G032564_T01 (Zea mays), 5'ss of exon 1
--GCTATCTCCTGGTCTGTCACCATGGTTCAGCGATTAACGTACCGTCGCCGCCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtac-actgc--cttccctctctctttgtcg--cgaattttctaggctacggat--ttcggcttagatatttcggcatcgtgttttggggtttggggccagcattgt
     | |  | ||   | ||  ||||| |||||  | || |||||    |||||| |||| ||||| || || || ||||||||||||||||||||||| ||||  || |   |||| | ||| | | ||||   ||    ||   | | | | |  | ||| ||    |  | ||  ||  | |     ||||  |      |||  
GAAACAGCGGCCGGC--GGCAAAATGGTGCAGCGGCTCACCTACCGGAAGCGCCACAGCTACGCCACAAAATCCAATCAGACCCGCGTGGTCAAGACCCCTGgtaagaccggcgcttcgcactcgcatggtcgattgatcgctcgttgtttctgttcgtgcgggttgtggaaataggattcccgctgatttgtttatgttgttgattag

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|18371260|gb|BJ202862.1|BJ202862
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|162248250|gb|FC423674.1|FC423674
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACGAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|162232416|gb|FC408837.1|FC408837
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACGAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|162207270|gb|FC383307.1|FC383307
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACGAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|67507470|gb|BJ940352.1|BJ940352
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACANAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|67578509|gb|BJ950676.1|BJ950676
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|67701409|gb|BJ961642.1|BJ961642
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|18326264|gb|BJ158263.1|BJ158263
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|67701253|gb|BJ961486.1|BJ961486
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|162231864|gb|FC408730.1|FC408730
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACGAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|162204474|gb|FC381702.1|FC381702
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACGAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|162277018|gb|FC453740.1|FC453740
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|67578368|gb|BJ950535.1|BJ950535
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|162225615|gb|FC401549.1|FC401549
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACGAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|67579273|gb|BJ951404.1|BJ951404
EST:     AAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGNCCGAAGT
genomic: AAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|67507937|gb|BJ940812.1|BJ940812
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|162244684|gb|FC423468.1|FC423468
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACGAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|18372122|gb|BJ203724.1|BJ203724
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|67579232|gb|BJ951377.1|BJ951377
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|37843088|gb|BJ601096.1|BJ601096
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|37842322|gb|BJ600330.1|BJ600330
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGGAGGGCAGCTGGGCCGAAG
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAA-GAGGGCAGCTGGGCCGAAG
EST: gi|37851424|gb|BJ609432.1|BJ609432
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGGAGGGCAGCTGGGCCGAAG
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAA-GAGGGCAGCTGGGCCGAAG
EST: gi|67578728|gb|BJ950895.1|BJ950895
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGNCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|67572937|gb|BJ945761.1|BJ945761
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT
EST: gi|162207271|gb|FC383308.1|FC383308
EST:     CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAG                         GTGGTAGGAATGTCTTCCAGACCGCCACGAAGAGGGCAGCTGGGCCGAAGT
genomic: CCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGT

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 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 25 (downstream exon)
Score: 21

GCTATCTCCTGGTCTGTCACCATGGTTCAGCGATTAACGTACCGTCGCCGCCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgtacactgcc ... tggcatgcagGTGGTAGGAATGTCTTCCAGACCGCCACAAAGAGGGCAGCTGGGCCGAAGTGTCCAGTGTCTGGAAAACGTATTGCTGGG




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