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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcgagtttgaatgtccaaattttatgtgatacgctgcacccgttacttaaaatataagcacgagtaaattcgtattttgattaatagaactatgcataatagatccgcactgagttcaatcatgctgatagtgatggaactcgggagctgtgcagGATGCCGGATACGAAACTATTATGATGAACTCGAACCCAGAGACCGTATCTACTGATTACGATACCTCTGATCGACTTTATTTCGAGCCTTTAACAGCGG

Basic information

species Physcomitrella patens
transcript PP1S343_21V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S343_21V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os01g38970.1 (Oryza sativa), 3'ss of exon 2
-----------gtacgcgagtttgaatgtccaaattttatgtgatacgctgcacc--cgttacttaaa-atataagcacg---agtaaattcgtatt-ttgattaatagaactatgcataatagatccgcactgagttcaatcatgctgatag--tgatggaac-tcgggagctgtgcagGATGCCGGATACGAAACTATTATGATGAACTCGAACCCAGAGACCGTATCTACTGATTACGATACCTCTGATCGACTTTATTTCGAGCCTTTAACAGCGG---
            | |    || |  |  |     |||| |   ||      ||     || | | ||| | | |||   |     | ||    |||  |  | ||    |  | |   ||| || |||    |  |||   | || ||||| |  | || |    |  | |    |  |  | || ||||| |||||||| ||||||||||| ||||||||||| || || ||||| || ||||||  ||| ||  | || || ||||| ||||| |  |   
gtttgtttctgcttcatttgtctccactttttggtttt-tacaattattaacatttttgtgattcaaataaacaagtctgccttatcaagctatatcatcaaataccgtatgttttgttaaaagttcctatatttgttatctaatactgatgggttaattgcttatttgcaatgatttatcagGCTGGATATGAAACTATAATGATGAACTCCAACCCAGAGACAGTTTCAACTGACTATGATACCAGTGACCGTTTGTACTTTGAGCCATTAACGGTTGAGG

upper sequence: PP1S343_21V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G061990_T01 (Zea mays), 3'ss of exon 2
gtacgcgagtttgaat-----gtccaaattttatgtgatacgctgcacccgttacttaaaatataagcacgagtaaattcgtattt---tgattaatagaactatgcataatagatccgcactga---gttcaatcatgctgatagtgatgg--aactcgggagctgtgcagGATGCCGGATACGAAACTATTATGATGAACTCGAACCCAGAGACCGTATCTACTGATTACGATACCTCTGATCGACTTTATTTCGAGCCTTTAACAGCGG---
||  |    |||| ||      | |  ||  | | | |           | | | ||  |   |      ||| || |  | ||||   |  | ||  | | |       || |  | | | |     ||       |  ||  | | |||     |||              | || |||||||| ||||||||||||||||| || || ||||| || |||||||| || ||||||  ||||||  | || || |||||  | ||||  |   
gtttgtttttttgcatcatttattcccatcctgtttcagtaatctttttcctcagttctagattgtttgtgagaaattgtgaattttcttagtcaaatgcattcaattgtatggccctgtatttttctgtatggctgttttggcactaatgttttgctcttttatctctttatagGCTGGATACGAGACTATTATGATGAACTCCAATCCTGAGACAGTCTCTACTGACTATGATACCAGTGATCGTTTGTACTTTGAGCCACTGACAGTTGAGG
















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|162247405|gb|FC421448.1|FC421448
EST:     AGGGAATTGAGTTCGATTACTGTTGCTGCCACGCAGCTTTCTCCCTTGGG                         GATGCCGGATACGAAACTATTATGATGAACTCGAACCCAGAGACCGTATCT
genomic: AGGGAATTGAGTTCGATTACTGTTGCTGCCACGCAGCTTTCTCCCTTGGGgtacgcgagt ... agctgtgcagGATGCCGGATACGAAACTATTATGATGAACTCGAACCCAGAGACCGTATCT
EST: gi|100414657|gb|BY956800.1|BY956800
EST:     AGGGAATTGAGTTCGATTACTGTTGCTGCCACGCAGCTTTCTCCCTTGGG                         GATGCCGGATACGAAACTATTATGATGAACTCGAACCCAGAGACCGTATCT
genomic: AGGGAATTGAGTTCGATTACTGTTGCTGCCACGCAGCTTTCTCCCTTGGGgtacgcgagt ... agctgtgcagGATGCCGGATACGAAACTATTATGATGAACTCGAACCCAGAGACCGTATCT
EST: gi|162190215|gb|FC366373.1|FC366373
EST:     AGGGAATTGAGTTCGATTACTGTTGCTGCCACGCAGCTTTCTCCCTTGGG                         GATGCCGGATACGAAACTATTATGATGAACTCGAACCCAGAGACCGTATCT
genomic: AGGGAATTGAGTTCGATTACTGTTGCTGCCACGCAGCTTTCTCCCTTGGGgtacgcgagt ... agctgtgcagGATGCCGGATACGAAACTATTATGATGAACTCGAACCCAGAGACCGTATCT
EST: gi|162166055|gb|FC340451.1|FC340451
EST:     AGGGAATTGAGTTCGATTACTGTTGCTGCCACGCAGCTTTCTCCCTTGGG                         GATGCCGGATACGAAACTATTATGATGAACTCGAACCCAGAGACCGTATCT
genomic: AGGGAATTGAGTTCGATTACTGTTGCTGCCACGCAGCTTTCTCCCTTGGGgtacgcgagt ... agctgtgcagGATGCCGGATACGAAACTATTATGATGAACTCGAACCCAGAGACCGTATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatccgcactgagttcaatcatgctgatagtgatggaactcgggagctgtgcagGATGCCGGATACGAAACTATTATGATGAACTCGAACCCAGAGACCGTATCTACTGATTACGATACCTCTGATCGACTTTATTTCGAGCCTTTAACAGCGG
                      tgctgat  putative branch site (score: 3)