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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaaattttacctcgatacctactcatctctgtcacgagtatggatggctaaggggtttagtttgttattcctaatggggggtatcctgaggttgttttagtagtctgatgaatggcttatcatcgacattttctgtattaacaattgtgggaaattactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACGCCTCTGTCTTTGGGTTTGGAGACGTTGGGTGGTGTGATGACGAAGATTA

Basic information

species Physcomitrella patens
transcript PP1S6_146V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S6_146V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os05g23740.1 (Oryza sativa), 3'ss of exon 6
gtttgaaattttacctcgatacctactcatctctgtcacgagtatggatggctaaggggtttagtttgttattcctaatggggggtatcctgaggttgttttagtagtctgatgaatggcttatcatcgacattttctgtattaacaattgtgggaaatt--actacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACGCCTCTGTCTTTGGGTTTGGAGACGTTGGGTGGTGTGATGACGAAGATTA
                                                                | | | | |  |  |   || |    |||   | || ||| |||| ||         ||   |    |  | | | ||     | ||    || ||  || |||||| || || ||| ||||||| || ||||||||||||||||| ||||| || || || ||| |||||||||||||  |||||||||||||||| |||||||
----------------------------------------------------------------tgtctcactggtgttctaggat----tgattatcttctag-agtcagaaagcaaatgtactctactgaactacagaatatctgactggcaaaattttgacaacagGCAGGAGTGTTGTCTGGTGATGTGAGCGACATTGTTCTTCTTGATGTAACACCACTTTCTCTGGGTTTGGAGACACTGGGTGGTGTGATGACCAAGATTA

upper sequence: PP1S6_146V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os12g14070.1 (Oryza sativa), 3'ss of exon 6
gtttgaaattttacctcgatacctactcatctctgtcacgagtatggatggctaaggggtttagtttgttattcctaatggggggtatcctgaggttgttttagtagtctgatgaatggcttatcatcgacattttctgtattaacaattgtgggaaattactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACGCCTCTGTCTTTGGGTTTGGAGACGTTGGGTGGTGTGATGACGAAGATTA
                                                || | || | || |  |||   | | | ||    |  |    | |  |||||     | |||||  |||  || |  ||| | || || ||| ||  |  ||||        ||  |||| ||| |||||||| || || || |  ||  | |||||||| ||||| || ||  ||||| | ||| |||||||||||||||| |||||||| |||||||
----------------------------------------------actgcccaaagcgtgt--tttaacactgccaa----gactgcatttatcttgttccg--aatctga--aat--ctcaa-atcaatatattttgtgtttccc-ttgta-------acaccagGGTGGAGTTTTGGCCGGAGATGTGAAAGATGTCGTTCTTCTTGATGTTACTCCATTGTCTCTTGGTCTGGAGACGTTGGGTGGAGTGATGACCAAGATTA

upper sequence: PP1S6_146V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G111475_T02 (Zea mays), 3'ss of exon 6
gtttgaaattttacctcgatacctactcatctctgtcacgagtatggatggctaaggggtttagtttgttattcctaatggggggtatcctgaggttgttttagtagtctgatgaatggcttatcatcgacattttctgtattaacaattgtgggaaattactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACGCCTCTGTCTTTGGGTTTGGAGACGTTGGGTGGTGTGATGACGAAGATTA
                                                |     ||  | | | | |  || |     |  |   |||| ||  |||| |     | |  | |  ||||  | |        ||||||| | |  || || |      |||||||||||||| |||||| ||||||| || ||||||||||| ||||| |||||||| ||  ||||  | |||||||||||  |||||||||| ||||| |||||||
------------------------------------------------ttttggagatgatcaatgtcctaat----gtatgttatatcttgtagttgctcctacattgcgtt--atggaatgtt-------ttttctg-agtgccatttttt-----ttactacagGCTGGAGTTTTGTCTGGTGATGTTAGCGACATTGTCCTTCTCGATGTGACCCCATTGTCCCTTGGTTTGGAGACACTGGGTGGTGTTATGACCAAGATTA

upper sequence: PP1S6_146V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G079668_T01 (Zea mays), 3'ss of exon 6
gtttgaaattttacctcgatacctactcatctctgtcacgagtatggatggctaaggggtttagtttgttattcctaatggggg--gtatcctgaggttgttttagtagtctgatgaatggcttatcatcgacattttctgtattaacaattgtgggaaattactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACGCCTCTGTCTTTGGGTTTGGAGACGTTGGGTGGTGTGATGACGAAGATTA
                                                          | ||||   | |   |||||||   |  ||| | ||  |||  |     | |    |  ||||  | |        |||||||  | |  | || |      |||||||||||||| ||| || ||||||| || ||||||||||| ||||| |||||||| ||  ||||  | |||||||||||  |||||||||| ||||| |||||||
---------------------------------------------------------agattagcaaggt---cctaatgaatgttgtagcttgcagttactcctacattgcatt--atggaatgtt-------ttttctgagtgacaagttttttttttttactacagGCTGGAGTTCTGTCTGGTGATGTTAGCGACATTGTACTTCTTGATGTGACCCCCTTGTCCCTAGGTTTGGAGACACTGGGTGGTGTCATGACCAAGATTA

upper sequence: PP1S6_146V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G001500_T02 (Zea mays), 3'ss of exon 6
gtttgaaatttta-cctcgatacctactcatctctgtcacgagtatggatggctaaggggtttagtttgttattcctaatggggggtatcctgaggttgttttagtagtctgatgaatggcttatcat-cgacattttctgtattaacaattgtgggaaattactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACGCCTCTGTCTTTGGGTTTGGAGACGTTGGGTGGTGTGATGACGAAGATTA
||       |||| |||| |       | || | ||    || ||   || |  |||  | ||   ||||  |   |          ||| | | | |||   || |   |  ||| |     |  || | ||||||   |||||     ||       |  ||  ||||  || |||||||| || || || |  ||  | |||||||||||||| || ||  | ||| | ||||||||||| |||||||| |||||||| |||||||
gtgattttctttatcctcaaatgtggtttatttttgcagagaata---atagtaaagttgctt---ttgtattgaattgcataacacatcattatgatgtaa-agcatcattttgactcatccaatatgccacatttggcgtattc-tgcttccattgcaacac--cagGGCGGGGTTTTGGCAGGAGATGTGAAAGATGTCGTTCTTCTGGATGTTACTCCATTATCTCTTGGTTTGGAGACATTGGGTGGAGTGATGACAAAGATTA

upper sequence: PP1S6_146V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA16G00410.1 (Glycine max), 3'ss of exon 5
gtttgaaattttacctcgatacctactcatctctgtcacgagtatggatggctaaggggtttagtttgttattcctaatggggggtatcctgaggttgttttagtagtctgatgaatggcttatcatcgacattttctgtattaacaattgtgggaaattac---tacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACGCCTCTGTCTTTGGGTTTGGAGACGTTGGGTGGTGTGATGACGAAGATTA
                   |      |    | | |||  | | |||| ||  |  | |  |  ||  |||  | |    | |  |   |  |   ||||||    || |  || || || ||| ||     | ||   || |     || | | || |||    |  |||||||||| |||||||| || |||||||||||||| ||  ||||||| || ||  | ||||||||| |||| ||  | |||||||||||||| || ||||
------------------gtgggatttggcttttatcattaat-tggaaggggacagagaatgtttgtttaagcttttcagtgtttgctcaaa---tgtttt----gttttgtggatagcatattatttttttgttaattaatgcttcttattgtaatttatgtttttagGCTGGTGTCTTGGCTGGAGATGTCAGCGACATTGTGCTGTTGGATGTCACTCCATTATCTTTGGGTCTGGAAACTCTAGGTGGTGTGATGACAAAAATTA

upper sequence: PP1S6_146V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv17s0000g03310.t01 (Vitis vinifera), 3'ss of exon 6
gtttgaaattttacctcgatacctactcatctctgtcacgagtatggatggctaaggggtttagtttgttattcctaatggggggtatcctgaggttgttttagtagtctgatgaatggcttatcatcg-acattttctgtattaacaattgtgggaaattactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACGCCTCTGTCTTTGGGTTTGGAGACGTTGGGTGGTGTGATGACGAAGATTA
                                                        | |||     |||  ||  |   |||  || ||  |||        | | || ||||| |  |    |||  |   | |    || |      ||   ||    | |||  ||||||||||||| |||| || ||||| |||||||| ||  |||||||| | ||  ||||| ||||| | ||||| ||||||||||| ||||| || || |
--------------------------------------------------------gtgttgtaaatgtagttttt---gggtagtttctggaga-------aatggtatgatgtacagaacctcactgtgaactaatcgtctatgtgttttccggttgatgcta--gGCTGGTGTTTTGTCTGGAGATGTCAGTGACATTGTGCTCTTGGATGTGTCTCCATTGTCTCTGGGTCTAGAGACATTGGGTGGTGTAATGACAAAAATCA

upper sequence: PP1S6_146V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv18s0041g01230.t01 (Vitis vinifera), 3'ss of exon 6
gtttgaaattttacctcgatacctactcatctctgtcacgagtatggatgg-ctaaggggtttagtttgttattcctaatggggggtatcctgaggt--tgttttagtagtctgatgaatggcttatcatcgacattttctgtattaacaattgtgggaaattactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACGCCTCTGTCTTTGGGTTTGGAGACGTTGGGTGGTGTGATGACGAAGATTA
||| |   | ||   ||     ||  || | | |   ||  || || |||  || | |   |||| |    |||  | ||||    |||  ||   |   | | ||||  ||   ||  ||| ||||  ||         || ||| ||| || |       || | |||||||||||||| ||||| || || ||  ||||||| ||  |||||||||| ||  ||||| |||||||||| ||  |||||||||| ||||| ||||| |
gttggtgctcttttttc-----cttttcttattttaaacttgtttgcatgttctgaagtccttagcta--cattgttgatggt---tattgtggaataaagatctagttttcctctgtttgg-ttattgtc--------ttgcattcacattttta------tatttcagGCTGGTGTTTTAGCTGGAGATGTTAGTAACATTGTGCTATTGGATGTGACACCATTGTCTCTGGGTTTGGAAACCCTGGGTGGTGTCATGACAAAGATCA

upper sequence: PP1S6_146V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ09963 (Selaginella moellendorffii), 3'ss of exon 7
gtttgaaattttacctcgatacctactcatctctgtcacgagtatggatggctaaggggtttagtttgttattcctaatggggggtatcctgaggttgttttagtagtctgatgaatggcttatcatcgacattttctgtattaacaattgtgggaaattactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACGCCTCTGTCTTTGGGTTTGGAGACGTTGGGTGGTGTGATGACGAAGATTA
                                                                                                     ||  | |||    ||| | |     | |  | |||   || | |  ||| |        | | ||||| |||||| ||||||| |||||||||||  | ||  | ||||| ||||| |||||||| ||||| ||||| ||| | || || || ||||||||||| |
----------------------------------------------------------------------------------------------------gtaaaaatctcggtaattggtc----ttggtacttt---tactgagtatttta-------atttcagGCCGGTGTTCTGGCTGGAGAAGTCAGCGATCTAGTGTTACTGGACGTGACTCCTCTGTCATTGGGCTTGGAAACGCTCGGAGGCGTTATGACGAAGATCA

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|162157845|gb|FC334116.1|FC334116
EST:     CGCTCTTGGAGCCGCAGTACAG                         GCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACG
genomic: CGCTCTTGGAGCCGCAGTACAGgtttgaaatt ... attactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACG
EST: gi|100443979|gb|BY982207.1|BY982207
EST:     ACGTGTCTGTGAACCCTGATGAGGTTGTCGCTCTTGGAGCCGCAGTACAG                         GCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACG
genomic: ACGTGTCTGTGAACCCTGATGAGGTTGTCGCTCTTGGAGCCGCAGTACAGgtttgaaatt ... attactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACG
EST: gi|162181462|gb|FC358076.1|FC358076
EST:     ACGTGTCTGTGAACCCTGATGAGGTTGTCGCTCTTGGAGCCGCAGTACAG                         GCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACG
genomic: ACGTGTCTGTGAACCCTGATGAGGTTGTCGCTCTTGGAGCCGCAGTACAGgtttgaaatt ... attactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACG
EST: gi|162246522|gb|FC419980.1|FC419980
EST:     ACGTGTCTGTGAACCCTGATGAGGTTGTCGCTCTTGGAGCCGCAGTACAG                         GCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACG
genomic: ACGTGTCTGTGAACCCTGATGAGGTTGTCGCTCTTGGAGCCGCAGTACAGgtttgaaatt ... attactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACG
EST: gi|162153649|gb|FC330185.1|FC330185
EST:     ACGTGTCTGTGAACCCTGATGAGGTTGTCGCTCTTGGAGCCGCAGTACAG                         GCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACG
genomic: ACGTGTCTGTGAACCCTGATGAGGTTGTCGCTCTTGGAGCCGCAGTACAGgtttgaaatt ... attactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatggcttatcatcgacattttctgtattaacaattgtgggaaattactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACGCCTCTGTCTTTGGGTTTGGAGACGTTGGGTGGTGTGATGACGAAGATTA
                           tattaac  putative branch site (score: 1)
                   attttctgtattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgaaattttacctcgatacctactcatctctgtcacgagtatggatggctaaggggtttagtttgttattcctaatggggggtatcctgaggttgttttagtagtctgatgaatggcttatcatcgacattttctgtattaacaattgtgggaaattactacagGCTGGTGTTTTGGCTGGTGAAGTCAGCGACATTGTTCTTCTGGATGTGACGCCTCTGTCTTTGGGTTTGGAGACGTTGGGTGGTGTGATGACGAAGATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA