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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttagtcttaccagtctttgtagaagtgaatggtgtttagtccgtgcacatggatcttcacgaactatcacgcatgttgacataagttgattgtcttctttccttcgtttataagacttgatgacttcatatgtgagtggtaaggatgtgtcttaccattaacatgtcttgttgtgattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACCAAGAAGCTTGAGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGG

Basic information

species Physcomitrella patens
transcript PP1S32_313V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S32_313V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 4
gtacttagtcttaccagtctttgtagaagtgaatggtgtttagtccgtgcacatggatcttcacgaactatcacgcatgttgacataagttgattgtcttctttcc-ttcgtttataagacttgatgacttcatatgtgagtggtaaggatgtgtcttaccattaacatgtcttgttgtgattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACCAAGAAGCTTGAGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGG
                                                                                               || || ||| | |||||   | |||   |   |||  || |     |  ||  | |  | |     | ||   | | |   ||  |||    |||| |||||| | || || ||    || ||||||||| ||||| | || || || ||||||||||| ||||||||||||||| | ||||||||| |  | |
-----------------------------------------------------------------------------------------------gtattttttgcattcgtacttgagaaaagtatact--atctaaagtttatagagctaaggccag--agtattttttttaaatgctatt----agGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACTAAAAAGCTTGAGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTG

upper sequence: PP1S32_313V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 4
gtacttagtcttaccagtctttgtagaagtgaatggtgtttagtccgtgcacatggatcttcacgaactatcacgcatgttgacataagttgattgtcttctttccttcgtttataagacttgatgacttcat-atgtgagtggtaaggatgtgtcttaccattaacatgtcttgttgtgattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACCAAGAAGCTTGAGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGG
                                                                                                       |  |  |  | |    |||| |   |     || |   |  | |  |||   || || |  ||    |  |||||         |||| |||||  |||| || ||    || ||||||||  | ||  | || || |||||||||||||||||||||||||||||| | ||||||||  |  | |
------------------------------------------------------------------------------------------------------gtattgtggctgtggttcttggttgttatgccatatccatactta--atggagctaac-accaatgaattctgttgct----tatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG
















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|162156032|gb|FC332199.1|FC332199
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|67693131|gb|BJ953364.1|BJ953364
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162169716|gb|FC345253.1|FC345253
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162169717|gb|FC345254.1|FC345254
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162172209|gb|FC348774.1|FC348774
EST:     GATAAA-TGNAAG                         GTCATGATTNTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCAC
genomic: GATAAATTG-AAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCAC
EST: gi|208396322|gb|DC920030.1|DC920030
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162249173|gb|FC420398.1|FC420398
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162252958|gb|FC429019.1|FC429019
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|208365127|gb|DC947335.1|DC947335
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162158826|gb|FC335349.1|FC335349
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162211540|gb|FC387620.1|FC387620
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162196282|gb|FC375391.1|FC375391
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|208396404|gb|DC920070.1|DC920070
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162223594|gb|FC399718.1|FC399718
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162188261|gb|FC364755.1|FC364755
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162188260|gb|FC364754.1|FC364754
EST:     TCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAA-TGNAAG                         GTCATGATTNTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCAC
genomic: TCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTG-AAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCAC
EST: gi|162196281|gb|FC375390.1|FC375390
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162187440|gb|FC362662.1|FC362662
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|208387159|gb|DC945458.1|DC945458
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162263938|gb|FC439207.1|FC439207
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162223593|gb|FC399717.1|FC399717
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|208365201|gb|DC931167.1|DC931167
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTNGAGTCAGGATAAGGACAGAGGCCGTAT
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTAT
EST: gi|18341631|gb|BJ173666.1|BJ173666
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|208392949|gb|DC928635.1|DC928635
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162249172|gb|FC420397.1|FC420397
EST:     GGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: GGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|67725166|gb|BJ975425.1|BJ975425
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGCATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|208389104|gb|DC945680.1|DC945680
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162187439|gb|FC362661.1|FC362661
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162244466|gb|FC422639.1|FC422639
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
EST: gi|162222297|gb|FC397109.1|FC397109
EST:     ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAG                         GTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC
genomic: ATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACC

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), 34 (downstream exon)
Score: 40

TGATATTGGAGGAGTCAGTGGCCTTCTGCATATCAGCCAAATTAGTCACGATCGCCTCACAACCGTTGAGACTGTACTCTCACCTGGAGATAAATTGAAGgtacttagtc ... gattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACCAAGAAGCTTGAGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgagtggtaaggatgtgtcttaccattaacatgtcttgttgtgattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACCAAGAAGCTTGAGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGG
                          cattaac  putative branch site (score: 40)
                           attaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttagtcttaccagtctttgtagaagtgaatggtgtttagtccgtgcacatggatcttcacgaactatcacgcatgttgacataagttgattgtcttctttccttcgtttataagacttgatgacttcatatgtgagtggtaaggatgtgtcttaccattaacatgtcttgttgtgattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACCAAGAAGCTTGAGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC