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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagactgttcgtattttgcatttcatgaatatgggcttcttgactagttgaaatcaggtgccagttatgcagtactttattattgcaccttcaaggttttagttgataatgtgattttgattttttcagcacggttgtgcaattaaatggatcttattggatgttggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAGAAGGAGGGCGTGCCTGAGGGTTTGTACATGTAGAGTATTCAGTACAGGT

Basic information

species Physcomitrella patens
transcript PP1S109_234V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 4
gtgagactgttcgtattttgcatttcatgaatatgggcttcttgactagttgaaatcaggtgccagttatgcagtactttattat-tgcaccttcaaggttttagttgataatgtgattttgattttttcagcacggttgtgcaattaaatggatcttattggatgttggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAGAAGGAGGGCGTGCCTGAGGGTTTGTACATGTAGAGTATTCAGTACAGGT
                                                                             ||||| || ||| |  |||  | ||  ||    ||       ||    |  ||  |||          |||    | | |   ||  |  || |    |||||||| || |  || ||||||||||| || ||||| |||||||  ||||||||||| || ||||| |||||| | |||||||   ||  ||| |    | 
-----------------------------------------------------------------------------tttataatgtgctcgctcattgattatgtctggaagaaacaatttgcatggtcctcacttccacattcttaccgtggtgt-gctgttttatgatttcacagGTGACACATGCTGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAGGAAGGTGTGCCGGAGGGTCTTTACATGTGATGTGCTCACTGGTCGC

upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 5
gtgagactgttcgtattttgcatttcatgaatatgggcttcttgactagttgaaatcagg--tgccagttatgcagtactttattattgcaccttcaaggttttagttg-----ataatgtgattttgattttttcagcacggttgtgcaattaaatggatcttattggatgtt-----ggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAGAAGGAGGGCGTGCCTGAGGGTTTGTACATGTAGAGTATTCAGTACAGGT
|| |  | | |  | ||||      ||      | |   ||| |    ||| |  | |    |  |    || |        | |  |      ||   |||| || ||     | ||  |  ||        | ||   |  |  |||| ||   |   |   ||| | ||||     | | ||  ||||||| || | ||||||||||||||| |||||||| || ||||  ||||||||||| || || || || ||  | || ||||     || ||  ||   |
gtaactcagctt-tgttttctcaaccagactccttgctctctagtactgttaatgttaaaactttcgagcatactaagtgccaatcctttcagatctgagtttgagctgcgctcagaacatatttgcatggaatgcaagtctttgttgcacttctcttt-ttacatttgctgttcttctgttgctttagGTGACACATGCCGATTTCAAGAAGGCCAAAGAGAAGGTCATGTTCAAGAAGAAGGAAGGTGTACCGGAAGGGCTTTATATGTGAGACATCCACCACTCAT

upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G095593_T02 (Zea mays), 3'ss of exon 1
gtgagactgttcgtattttgcatttcatgaatatgggcttcttgactagttgaaatcaggtgccagttatgcagtactttattattgcaccttcaaggttttagttgataatgtgattttgattttttcagcacggttgtgcaattaaatggatcttattggatgttggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAGAAGGAGGGCGTGCCTGAGGGTTTGTACATGTAGAGTATTCAGTACAGGT------------------------------------
                                                                                                           |||  |  | || ||| |  | ||    ||| ||  |||   || || || |||  |   |  |   |||||||| || |  |||||||||||||| || ||||| |||||||| ||||||||||| || || || || ||| | |||||||||   ||  | |     |                                    
-----------------------------------------------------------------------------------------------------------atatagc-acttcgatctgattag----gttctgagatttgctg-atgtttttgttttgggtacacccaggtgacccatgcagatttcaagaaggcaaaggagaagGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGCCAATCTATTCATCATGCCGAACAAGTTACCCGATTGTGTGTGTACTAGCAC

upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 4
gtgagactgttcgtattttgcatttcatgaatatgggcttcttgactagttgaaatcaggtgccagttatgcagtactttattattgcaccttcaaggttttagttgataatgtgattttgattttttcagcacggttgtgcaattaaatggatcttattggatgttggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAGAAGGAGGGCGTGCCTGAGGGTTTGTACATGTAGAGTATTCAGTACAGGT
                                                                           | ||   ||    | ||     || |   | ||  ||   | || ||| |  | ||    ||| ||  |||   || || || |||  |   |  |   |||||||| || |  |||||||||||||| || ||||| |||||||| ||||||||||| || || || || ||| | |||||||||   ||  | |     |
------------------------------------------------------------------------tccatttgcatagcataactgtcttgtctacttggaatatagcacttcgatctgattag----gttctgagatttgctg-atgtttttgttttgggtacacccagGTGACCCATGCAGATTTCAAGAAGGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGCCAATCTATTCATCAT

upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 5
gtgagactgttcgtattttgcatttcatgaatatgggcttcttgactagttgaaatcaggtgccagttatgcagtactttattattgcaccttcaaggttttagttgataatgtgattttga--ttttttcagcacggtt-gtgcaattaaatggatcttattggatgttggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAGAAGGAGGGCGTGCCTGAGGGTTTGTACATGTAGAGTATTCAGTACAGGT
                                                                          || | | |   | | | ||      | | ||| ||||| | ||||  |  |||||||  | |  ||  ||  ||    |   | ||| |  || ||||||    |||||||||| | ||| || |||||||| || || |||||||||| ||||||||| || || |||||||| ||  |||| ||||  |  | |     |   |
--------------------------------------------------------------------------taatgtttatcttctctttggcttgtattgtttataatataatttgaagtttttttctccccaatttatgatatcttcttactattact--attttggtc----agGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAAAACTATCCTCTATT

upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 5
gtgagactgttcgtattttgcatttcatgaatatgggcttcttgactagttgaaatcaggtgccagttatgcagtactttattattgcaccttcaaggttttagttg---ataatgtgattttgattttttcagcacggttgtgcaattaaatggatcttattggatgttggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAGAAGGAGGGCGTGCCTGAGGGTTTGTACATGTAGAGTATTCAGTACAGGT
                                                                              |  ||| ||    |    |||||   |||   ||||| | ||||  | |||||   | |     |  |  | |     ||||| |     ||  |  | ||||||||||| | ||| || |||||||| || || |||||||||| ||||||||| || || |||||||| ||  |||| ||||  | || |     |    
------------------------------------------------------------------------------tgtttaatgtgtatctttggtttgtattgtatataatataatttgaagttttttttctccccaattta--tgatatcttcttactattacttttttgttcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAATACTATCCTCTATC

upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EDP05705 (Chlamydomonas reinhardtii), 3'ss of exon 10
gtgagactgttcgtattttgcatttcatgaatatgggcttcttgactagttgaaatcaggtgccagttatgcagtactttattattgcaccttcaaggttttagttgata--atgtgattttgattttttcagcacggttgtgcaattaaatggatcttattggatgttggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAGAAGGAGGGCGTGCCTGAGGGTTTGTACATGTA----GAGTATTCAGTACAGGT-----
                                                                     ||||| |       | |||     | |||       |||     ||||   |  ||    |   | ||  |  ||        ||  | | ||| | | ||   |||||||          ||| |||   ||||| || ||||| ||| | || |||||||||||||||||||| ||||| |||||||||||    | | || ||  ||         
--------------------------------------------------------------------ctgcagca-------actgcttgcacgagggcgcgcatgacgccgtgtgccgtacatggacttgtctcgactccgcgccc----ggcccatcttgcacgctgcctctgcagGC---------CGACTTCCGCAAGGCCAAGGAGAAGGTGCTCTACAAGAAGAAGGAGGGCGTGCCGGAGGGGTTGTACATGTAATGGGGGGATGCAAGACGACGACAGA

upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 5
gtgagactgttcgtattttgcatttcatgaatatgggcttcttgactagttgaaatcaggtgccagttatgcagtactttattattgcaccttcaaggttttagttgataatgtgattttgat-tttttcagcacggttgtgcaattaaatggatcttattggatgttggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAGAAGGAGGGCGTGCCTGAGGGTTTGTACATGTAGAGTATTCAGTACAGGT-
                                                                                                               |    | | |||  ||||||  ||  |  || ||       ||| || ||         | || ||||| |||||||  |||||||||||||| |||||||| || ||||| |||||||| || ||||| || |||||  |||||||||| | ||  |    ||| | 
--------------------------------------------------------------------------------------------------------------gtagtttctcgatgcttttcacaactttcttgtaac------gattttcttc--------ttctccagGTAACTCAAGCTGATTTCAAGAAGGCGAAAGAGAAGGTCATGTACAAGAAGAAAGAAGGCGTCCCGGAGGGCCTGTACATGTA-AATAGCCGTCCCAGCTT

upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 5
gtgagactgttcgtattttgcatttcatgaatatgggcttcttgactagttgaaatcaggtgccagttatgcagtactttattattgcaccttcaaggttttagttgataatgtgattttgattttttcagcacggttgtgcaattaaatggatcttattggatgttggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAGAAGGAGGGCGTGCCTGAGGGTTTGTACATGTAGAGTATTCAGTACAGGT-
                                                                                                                         | ||| |||   |  ||   ||| |   | |     |||   |  |  | || ||||| |||||||  |||||||||||||| |||||||| || ||||| |||||||| || ||||| || |||||  |||||||||| | ||  ||   ||| | 
-----------------------------------------------------------------------------------------------------------------------gtagtttctcaatgctttt-cacaactttcttgtaacgatt---ttcttcttctccagGTAACTCAAGCTGATTTCAAGAAGGCGAAAGAGAAGGTCATGTACAAGAAGAAAGAAGGCGTCCCGGAGGGCCTGTACATGTA-AATAGCCATCCCAGCTT

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|37852217|gb|BJ610225.1|BJ610225
EST:     CTATCTGTACGGAAGCTGGTCTTCTTGCATTGCGTGAGCGCCACATGAAG                         GTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAG
genomic: CTATCTGTACGGAAGCTGGTCTTCTTGCATTGCGTGAGCGCCGCATGAAGgtgagactgt ... ggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAG
EST: gi|67694035|gb|BJ954268.1|BJ954268
EST:     CTATCTGTACGGAAGCTGGTCTTCTTGCATTGCGTGAGCGCCGCATGAAG                         GTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAG
genomic: CTATCTGTACGGAAGCTGGTCTTCTTGCATTGCGTGAGCGCCGCATGAAGgtgagactgt ... ggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAG
EST: gi|162186727|gb|FC362763.1|FC362763
EST:     CTATCTGTACGGAAGCTGGTCTTCTTGCATTGCGTGAGCGCCGCATGAAG                         GTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAG
genomic: CTATCTGTACGGAAGCTGGTCTTCTTGCATTGCGTGAGCGCCGCATGAAGgtgagactgt ... ggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAG
EST: gi|37849561|gb|BJ607569.1|BJ607569
EST:     CTATCTGTACGGAAGCTGGTCTTCTTGCATTGCGTGAGCGCCACATGAAG                         GTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAG
genomic: CTATCTGTACGGAAGCTGGTCTTCTTGCATTGCGTGAGCGCCGCATGAAGgtgagactgt ... ggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAG
EST: gi|37830407|gb|BJ588419.1|BJ588419
EST:     CTATCTGTACGGAAGCTGGTCTTCTTGCATTGCGTGAGCGCCGCATGAAG                         GTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAG
genomic: CTATCTGTACGGAAGCTGGTCTTCTTGCATTGCGTGAGCGCCGCATGAAGgtgagactgt ... ggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttcagcacggttgtgcaattaaatggatcttattggatgttggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAGAAGGAGGGCGTGCCTGAGGGTTTGTACATGTAGAGTATTCAGTACAGGT
                    aattaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagactgttcgtattttgcatttcatgaatatgggcttcttgactagttgaaatcaggtgccagttatgcagtactttattattgcaccttcaaggttttagttgataatgtgattttgattttttcagcacggttgtgcaattaaatggatcttattggatgttggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAGAAGGAGGGCGTGCCTGAGGGTTTGTACATGTAGAGTATTCAGTACAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG