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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcatcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt...

Basic information

species Physcomitrella patens
transcript PP1S47_161V6.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagc-atcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccattt--cggtactaggtt----------
 ||||||||||||||||||||||||||||| || ||||||||||| || || || || ||  | || ||  | | |  | |  |  |   ||||||| |||||  | |    |   ||   |||   || ||| || ||  ||      |  ||      | | ||  || || | ||  | |  | |   || || | |             
CATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAATTTGGAGAACATATTCGGTCAAGCTCCTGGTGTTGATTCGgtacaatctgataacctagctttcatttgctcaaaaccttttttccattataaccgatcttacgtttccatatgttgacatgctgactcgccgttatttgacaatctctccag

upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: LOC_Os01g46750.1 (Oryza sativa), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgag--catc-actttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt-----------------------------------------------------------------
 || |||||||| ||||| |||||||||||||| ||||||||||| || ||||| |||||  | || ||  | ||   |      ||  || | ||| ||||||  |   |||  |||||   ||||    | | |||  |  |||| || ||    |    ||| ||    |  |   |  |  |   |  |  | ||  ||                                                                 
CATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAATTTGGAGAACATTTATGGTCTTGTTTCTGCTATAGATTCGgtatatggctatctgctttaaagttctctgctccttaaatttattct-gcgacattgttt-ttgcctttttggtatcataaatgactgatgggtcattaccttctgtttctgctaaaacaatttgaaaaactttcctctgttttttttttttttgaacatctgttcag

upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: LOC_Os06g06350.2 (Oryza sativa), 5'ss of exon 11
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcatcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt-
 |||||  | ||||| || || ||||||||||| || |||||||| |||||||| ||||| || || |||||||||   |    |       | ||| |||||    |   |||  || | ||   | ||||     | ||          |  |      ||          |   | | || |||    | |     | 
CATTGACAGGAAGAAAAATATATTCAAGCTTTCACAGGGAGAATATGTTGCAGTAGAAAATCTCGAGAATGTGTACGGGGTTCTCCAAGAGATAGATTCGgtaactactatacta-actactcactttttcaggggatcgtctcaaattttatgtttctatctgatatgagcctttttttccctattatatttcccatatg

upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagc---atcactttacgattctgctgttca--taatctagttcttgcaaccacatgcactgctttagcagatttcga--tctacccatttcggtactaggtt
 ||||| ||||||||||||||||||||||| || || ||||| |||||||| || || || || || ||  | |    | |  |  |  |||||||| |||||        | || | | |   |   | ||  |  |  |||    |        |||   | | |  ||    || || |  ||||  |  | |      ||   
CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctcaaaacagtcttcatctacacagtctaagtgttctgcagcaaatggttacaaataattccataatccatctctaagtctaaacgatacatcttcag---

upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: GRMZM5G812228_T01 (Zea mays), 5'ss of exon 11
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatg-agca---tcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttc---ggtactaggtt
 |||||| | |||||||| || ||||||||||| || || |||||||||||||| ||||| || || ||||||||   ||          | | ||| ||||||| | ||   |||||  |  || |  | ||    | | |  |||         ||        |||   |   |||| |  ||||||      ||| || |   
GATTGATAGAAAGAAGAATATTTTCAAGCTTTCGCAGGGGGAATACGTTGCAGTGGAAAATCTAGAGAATGTGTATGGTGTTCTTCAAGATATAGATTCGgtatgtaacaaactcactggaaaatgc-acggtcttaactttttttccccatgttgcaacagaattttttata---ttcgtttcacccatgcttaaggtgcttg---

upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagc-atcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt---
||||||||| |||||||| || || |||||||| ||||||||||| ||||| ||||||||||| || ||| | |||  | |    || ||| ||||  | |||||  |   | | | |  || ||  |  |   |||   ||| | |   ||  |      |  | |    ||| | |    |  |||     | || ||    
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctgactcctgagaatcctattccttccaat--ggttttggtgtcctaacttgtag--taaatttattaccaaaatcaaattggaaaaataagtagaa

upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: GLYMA11G02030.1 (Glycine max), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcatcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatt--tcgatctacccatttcggtactaggtt
||||||||| |||||||| || || |||||||| ||||||||||| ||||| ||||||||||| || ||| | |||  | |    || ||| ||||  | |||||  | | |   | | ||||         |   | |||  | |        ||  ||   ||||    ||  |  || | | ||||  |    |  || 
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcc-tgagaatcctattccttccaatgtcccccagtattggtgcatgt-tgatctatattagtgatttagtgaatgtccacattctgtagttcagta

upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: GLYMA05G36910.1 (Glycine max), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTG-------ATGCGgtatgagcatcactttacgattctgctgttcataatctagttct---tgcaaccacatgcactgcttta--gcagatttcgatctacccatttcggtactaggtt----------------------------------------------------------------
||||||||| |||||||| || || |||||||| ||||||||||| ||||| || |||||||| || ||| | ||   | |  | || |||||||       |||   | ||| |    || |   | ||  ||  || |    |  || |   ||  | || | |   || ||||  ||| |  | |    |    |||  ||   || ||                                                                
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAACCTGGAGAATATTTATGTTCAAGCTTCTTCTGTTGAATCTgtatgtcttgtgaacccttctcttttaatcaacttatc-tgccttcattatgaatgatatcaaaaggtttggtttactgcaaagatagtaacaaaggttttagtttcagcttcatttcatgagcagataatgttccgtgatatgttgatattacttcttttccaactctatttcag

upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: AT1G49430.1 (Arabidopsis thaliana), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcatcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgct--ttagcagat-ttcgatctacccatttcggtactaggtt
 || ||| | |||||||||||||||||| | |||||||| ||||| ||||| || |||||||| |||||    |||      |   ||    ||| |  ||||||   || |  |||  ||| || | |  ||| | || |  | | ||    ||  | || |   ||  |  | | | ||||||| ||    ||   ||   
CATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAACCTCGAAAACACTTACTCAAGATGTCCCCTCATTGCTCAGgtatgta-atta--ttaaaattatgttttcaatactataatcatagtaattgaata-attgttatctaataattgtactatctaccaataattgtgacag---

upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: AT1G64400.1 (Arabidopsis thaliana), 5'ss of exon 14
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcatcactttacgattct--gctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt
 || || || |||||||||||||| || || |||||||||||||||||||| || || ||| | || ||  | |||| | |   | || |  ||||  |||||| ||  | |   ||  | |||    |   | | |  ||   |||  | | | |||  ||| |  | ||  || |                         
CATCGACCGTAAGAAGAACATCTTTAAACTGTCTCAAGGAGAATACGTTGCCGTTGAGAACTTGGAGAACATATACAGTCATGTCGCCGCCATTGAATCGgtattagt-tgaaaatataactcttaagtaaccgttacataaaactt--agcta-atgatctgttaaaacattttgcag-----------------------

upper sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatga---------gcatcactttacgattctgctg--ttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt
||| || |||||||||||||| ||||||||||| ||||||||||||||||| || || ||| | |||||  | ||   |      ||   | ||||  |||||||          |  |||   |||| ||   |||  || || |     || || |  |    |    | || |  ||| ||||  | |       ||           
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttttacctgaatttatcactcctttttttcccctgattttggttctctctcag-tttcattgtgtatgcctct----------

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|162149872|gb|FC326195.1|FC326195
EST:     CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCG                         ATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC
genomic: CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcat ... gcgtgcacagATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC
EST: gi|162196991|gb|FC375216.1|FC375216
EST:     CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCG                         ATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC
genomic: CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcat ... gcgtgcacagATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC
EST: gi|162167247|gb|FC342812.1|FC342812
EST:     CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCG                         ATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC
genomic: CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcat ... gcgtgcacagATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC
EST: gi|162194188|gb|FC371039.1|FC371039
EST:     CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCG                         ATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC
genomic: CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcat ... gcgtgcacagATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC
EST: gi|162177647|gb|FC353233.1|FC353233
EST:     CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCG                         ATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC
genomic: CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcat ... gcgtgcacagATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC
EST: gi|162177648|gb|FC353234.1|FC353234
EST:     CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCG                         ATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC
genomic: CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcat ... gcgtgcacagATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC
EST: gi|162151929|gb|FC328890.1|FC328890
EST:     CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCG                         ATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC
genomic: CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcat ... gcgtgcacagATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC
EST: gi|67692540|gb|BJ952773.1|BJ952773
EST:     CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCG                         ATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC
genomic: CAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcat ... gcgtgcacagATTTGGGTTTATGGAAACAGTTTCGAATCGTTTCTGGTGGCTGTAGCAGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagcatcactttacgattctgctgttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC