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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgataaaatgaccaaaaccttcattggtctctctctctttctctctctttctctctctacctcacagatatcgacgtcaagtgaaaattttggactaaactagcagaagaccttgcgcttgacccagtttcaaagcatcgagatttgactaagaataaaatcactgtggttttttagATCCTAAGTACATGATTCGAGCGATACCGAGCAATGCTTCTGACAATGTCTATTGCACCTTGCTCGCTCATGGTGCGATTCATGGAGCCATGGCTGGTTA

Basic information

species Physcomitrella patens
transcript PP1S131_40V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S131_40V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 12
gtatgataaaatgaccaaaaccttcattggtctctctctctttctctctctttctctctctacctcacagatatcgacgtcaagtgaaaattttggactaaactagcagaagaccttgcgcttgacccagtttcaaagcatcgag--atttgactaagaataaaatcactgtggttttttagATCCTAAGTACATGATTCGAGCGATACCGAGCAATGCTTCTGACAATGTCTATTGCACCTTGCTCGCTCATGGTGCGATTCATGGAGCCATGGCTGGTTA
                                                                                   || |   | ||    |  ||| |  |||  |  ||    |     | ||  |     || ||  || |||  |||        || | |  || | ||||||| |  |||||||| || || || || |||||||| || |||||||||||||||||| ||||||| ||| |||| |||||||| || ||||| || ||
-----------------------------------------------------------------------------------gtaatcgtcttcttttttacttggtgaacgcagtgttagtttgtaatttatagcatgtcaaggaatctgatgaagtgcctg-ccattttt-ttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA

upper sequence: PP1S131_40V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 12
gtatgataaaatgaccaaaaccttcattggtctctctctctttctctctctttctctctctacctcacagatatcgacgtcaagtgaaaattttggactaaactagcagaagaccttgcgcttgacccagtttcaaagc----atcgagatttgactaagaataaaatcactgtggttttttagATCCTAAGTACATGATTCGAGCGATACCGAGCAATGCTTCTGACAATGTCTATTGCACCTTGCTCGCTCATGGTGCGATTCATGGAGCCATGGCTGGTTA
                                                                                                         |     |   ||   |     |   |||||  ||    |  |  | ||    |    | | ||   | |  |  |  |||||| | ||||||||| || || || || |||||||||||||| || |||||||||||  |||| |||||  | | | | ||||||||||||||||| ||
---------------------------------------------------------------------------------------------------------gtcagtggttttcttcggtgtcatatttcagggccagaactgctagttacacacatctcagatgtttcttctactgcagATCCAACGTACATGATACGTGCCATCCCAAGCAATGCTTCTGATAACGTCTATTGCACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATA

upper sequence: PP1S131_40V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 11
gtatgataaaatgaccaaaaccttcattggtctctctctctttctctctctttctctctctacctcacagatatcgacgtcaagtgaaaattttggactaaactagcagaagaccttgcgcttg-acccagtttcaaagcatcga--gatttgactaagaataaaatcactgtggttttttagATCCTAAGTACATGATTCGAGCGATACCGAGCAATGCTTCTGACAATGTCTATTGCACCTTGCTCGCTCATGGTGCGATTCATGGAGCCATGGCTGGTTA
                                                                                                       | | | |     |    ||   |   ||   |   |||  |   | | | || |||      |    | | || | | |||||||| ||| ||||| || ||  | || |||||||| ||||||||||||||||||||  | || |||||  ||||  |||||||||| ||||| || ||
-----------------------------------------------------------------------------------------------------gtttgtatacactatctttctaatatatagaagctgggcaatggctggtctaaccaagtgctgcact--ttttgtctatcagATCCTACGTATATGATCCGTGCTGTTCCAAGCAATGCATCTGACAATGTCTATTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGGTA

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|67693166|gb|BJ953399.1|BJ953399
EST:     GATCATTTCCAGGCAGAGTTTAGGGAAACGCTTAACCTGAAGTACATAG                         ATCCTAAGTACATGATTCGAGCGATACCGAGCAATGCTTCTGACAATGTCT
genomic: GATCATTTCCAGGCAGAGTTTAGGGAAACGCTTAACCTGAAGTACATAGgtatgataaa ... ggttttttagATCCTAAGTACATGATTCGAGCGATACCGAGCAATGCTTCTGACAATGTCT
EST: gi|162277927|gb|FC454058.1|FC454058
EST:     GATCATTTCCAGGCAGAGTTTAGGGAAACGCTTAACCTGAAGTACATAG                         ATCCTAAGTACATGATTCGAGCGATACCGAGCAATGCTTCTGACAATGTCT
genomic: GATCATTTCCAGGCAGAGTTTAGGGAAACGCTTAACCTGAAGTACATAGgtatgataaa ... ggttttttagATCCTAAGTACATGATTCGAGCGATACCGAGCAATGCTTCTGACAATGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccagtttcaaagcatcgagatttgactaagaataaaatcactgtggttttttagATCCTAAGTACATGATTCGAGCGATACCGAGCAATGCTTCTGACAATGTCTATTGCACCTTGCTCGCTCATGGTGCGATTCATGGAGCCATGGCTGGTTA
                    atttgac  putative branch site (score: 4)
                                               tttttt  putative PPT
                         actaagaataaaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgataaaatgaccaaaaccttcattggtctctctctctttctctctctttctctctctacctcacagatatcgacgtcaagtgaaaattttggactaaactagcagaagaccttgcgcttgacccagtttcaaagcatcgagatttgactaagaataaaatcactgtggttttttagATCCTAAGTACATGATTCGAGCGATACCGAGCAATGCTTCTGACAATGTCTATTGCACCTTGCTCGCTCATGGTGCGATTCATGGAGCCATGGCTGGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA