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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaccatattttttagatgcattgtatagactttccgttccgccttagactctcaagctttcaacttcaaatggtttttgttggttcgaaccgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG

Basic information

species Physcomitrella patens
transcript PP1S277_10V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S277_10V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA10G30220.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------tagaccatat-tttttagatgcattgtatagactttccgttccgccttagactctcaagctttcaacttcaaatggt--ttttgttggttcgaaccgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG
                                               || ||| | |  | ||     |  | | | | |  |     | |    |    ||  |  || ||  | ||  || |   ||  |   | |          ||||||| ||||| || ||| ||||  | ||||||||||||||||||||| |||||||||| ||  |  |||| |
gtaagctgtttttacttccagtcatggtgtgcattcttcttcatctctaaaccctgtactcttcctctctcttttttggccatgaaacctgtaccattgactttattttccatgtgcatttgataacttcttcaatacttggatgactagGTGGGTGCAGAAAACAATCTACTTGTGAAGGATCACACTCACACTTTTGTTAACAAAGGGGGTCAAATTGGTG

upper sequence: PP1S277_10V6.3 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA20G37170.1 (Glycine max), 3'ss of exon 3
--------------------------------------tagaccatattttttagatgcattgtatagactttccgttccgcct----tagactctcaagctttcaacttcaaatggtttttgttggttcgaaccgtta-----cagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG
                                      |   || | |||||| |          |  ||| |    |     |    |  ||  |  | || || | ||  |||   || |  |  ||| |  | |        ||||||| || || || ||| ||||  | ||||||||||||||||||||| |||||||||| ||  |  ||||||
gtaagctgtttttacttcatctctaaaacctgttttcttcttccctcttttttggccatgaaacctgtactattgactttatttttcgtgtacattgtatctgtccattt--aataacttctacttcttcaatgcttggatgactagGTGGGTGCGGATAACAATCTACTTGTAAAGGATCACACTCACACTTTTGTTAACAAAGGGGGTCAAATTGGAG
















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|162165520|gb|FC340631.1|FC340631
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162155413|gb|FC332027.1|FC332027
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162170376|gb|FC346781.1|FC346781
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|18327722|gb|BJ159725.1|BJ159725
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162151154|gb|FC327153.1|FC327153
EST:     CAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: CAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162198693|gb|FC373474.1|FC373474
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162168664|gb|FC343926.1|FC343926
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162176795|gb|FC352809.1|FC352809
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
EST: gi|162166539|gb|FC343236.1|FC343236
EST:     TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAG                         GTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT
genomic: TACATGTCTTTTTCGGGTGCTACAACAATCTGTTTCGCCTCCTAGCTAAGgtactttcac ... accgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagactctcaagctttcaacttcaaatggtttttgttggttcgaaccgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG
                              tttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaccatattttttagatgcattgtatagactttccgttccgccttagactctcaagctttcaacttcaaatggtttttgttggttcgaaccgttacagGTGGGGGCAGACAATAATTTACTACTCAAGGATCACACTCACACTTTTATTAACAAAGGCGGCAACGTTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG