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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAGAAGCATACCCTTCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccacttcgttttgcttgattctttttgacttgttgaatctagctgtgtttgtccgagtgcttttcctcggcattttagggggcgtctgtgattttg...

Basic information

species Physcomitrella patens
transcript PP1S6_198V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S6_198V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ07113 (Selaginella moellendorffii), 5'ss of exon 2
AAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAGAAGCATACCCTTCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccacttcgttttgcttgattctttttga-cttgttgaatctagctgtgtttgtccgagtgcttttcctcggcattttagggggcgtctgtgattttg
||||||||||||||||||||||  || |||   |||  |||||| || || |||||||| ||||||||||||||||| ||||||||| | |||| ||||||||        |    |   ||||  |   || |||| |     | || |||    ||  ||                                       
AAGACGAAGAAGTCCTTCTGCCAAGGGAAGAATTGCCGGAAGCACACGCTCCACAAGGTCACGCAGTACAAGAAGGGCAAGGACAGCCTCTACGTCCAAGgtaa-------gagccggaagatttctcgcgagcttgctctgaattgcggtgaggttcacag---------------------------------------

upper sequence: PP1S6_198V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ05955 (Selaginella moellendorffii), 5'ss of exon 2
AAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAGAAGCATACCCTTCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccacttcgttttgcttgattctttttga-cttgttgaatctagctgtgtttgtccgagtgcttttcctcggcattttagggggcgtctgtgattttg
||||||||||||||||||||||  || |||   |||  |||||| || || |||||||| ||||||||||||||||| ||||||||| | |||| ||||||||        |    |   ||||  |   || | || |     | || |||    ||  ||                                       
AAGACGAAGAAGTCCTTCTGCCAAGGGAAGAATTGCCGGAAGCACACGCTCCACAAGGTCACGCAGTACAAGAAGGGCAAGGACAGCCTCTACGTCCAAGgtaa-------gagccggaagatttctcgcgagcgtgctctgaattgcggtgaggttcacag---------------------------------------
















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|67709844|gb|BJ965660.1|BJ965660
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|7582814|gb|AW699031.1|AW699031
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162248096|gb|FC420101.1|FC420101
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|18369053|gb|BJ201138.1|BJ201138
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGANGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|7147838|gb|AW509760.1|AW509760
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162250013|gb|FC427114.1|FC427114
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162209881|gb|FC386023.1|FC386023
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|37847272|gb|BJ605280.1|BJ605280
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162202561|gb|FC379244.1|FC379244
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162245704|gb|FC419604.1|FC419604
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|15729018|gb|BI741095.1|BI741095
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|18327147|gb|BJ159148.1|BJ159148
EST:     TCACAAGGTGACGCAGTACGAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|18369077|gb|BJ201162.1|BJ201162
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162253005|gb|FC429066.1|FC429066
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|18366870|gb|BJ198950.1|BJ198950
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162202562|gb|FC379245.1|FC379245
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162213753|gb|FC390368.1|FC390368
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|15327299|gb|BI487887.1|BI487887
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162253004|gb|FC429065.1|FC429065
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|18335425|gb|BJ167444.1|BJ167444
EST:     TCACAAGGTGACGCAGTACGAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162203006|gb|FC380078.1|FC380078
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|67572978|gb|BJ945802.1|BJ945802
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162245986|gb|FC421875.1|FC421875
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162209880|gb|FC386022.1|FC386022
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162211965|gb|FC388045.1|FC388045
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|7047264|gb|AW477158.1|AW477158
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|67703412|gb|BJ963645.1|BJ963645
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|6102360|gb|AW126830.1|AW126830
EST:     CACAAGGTGACGCAGGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATG
genomic: CACAAGGTGACGCAG-TACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATG
EST: gi|67723922|gb|BJ974181.1|BJ974181
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|15320178|gb|BI487827.1|BI487827
EST:     CAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: CAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162213754|gb|FC390369.1|FC390369
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162249941|gb|FC427042.1|FC427042
EST:     AAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: AAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|37850368|gb|BJ608376.1|BJ608376
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|67696359|gb|BJ956592.1|BJ956592
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
EST: gi|162203414|gb|FC378822.1|FC378822
EST:     TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAG                         GAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC
genomic: TCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 91

AAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAGAAGCATACCCTTCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccactt ... attccggcagGAAAGAGGCGTTATGATAGGAAGCAGTCGGGTTACGGAGGTCAGACCAAGCCCGTCTTTCACAAGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAGAAGCATACCCTTCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCTTGTACGCCCAAGgtatccacttcgttttgcttgattctttttgacttgttgaatctagctgtgtttgtccgagtgcttttcctcggcattttagggggcgtctgtgattttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG