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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgattgctgcgaaatgattactgtctcctggactttaactaattgtcctcagtttgcgacgatctaggcgaagtcaatcctccgcaaagtggcagaagttcgctaaccatctcaaccgtaagggtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTGAAGCTCAAAGAAGACTATTACGTCATGGATCCCTACAAAGCAGTGGAGC

Basic information

species Physcomitrella patens
transcript PP1S68_116V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S68_116V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G017110_T01 (Zea mays), 3'ss of exon 3
gtacgattgctgcgaaatgattactgtctcctggactttaactaattgt-cctcagtttg-cgacgatctaggcgaagtca--atcctccgcaaagtggcagaagttcgctaaccatctcaaccgtaagggtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTGAAGCTCAAAGAAGACTATTACGTCATGGATCCCTACAAAGCAGTGGAGC
                                | ||| |   |   ||| |  | ||| | ||||||||    || |  |    |      ||| ||| | |||   |||   |  |      |||    | |     ||||||||||||||||||||||||| ||||| || ||||||||    ||||| |||||   |||||  || ||||||||||| |||  ||| || || ||| 
--------------------------------gtactctgtgtccgtgtacaactgttggtcgacgatcagatcgtaaccgccgtgtgtaacaatgtgtctgaaagacgc---ctttggtggtcgtttctgatgtcctagGTCTGCTGGGAGAAGTTTGCAAGGTATTTTGAGGTGGAGCTGAAGGAGGTTAAGCTATCAGAAGGGTACTACGTCATGGACCCCGTCAAGGCTGTTGAGA

upper sequence: PP1S68_116V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G098875_T02 (Zea mays), 3'ss of exon 3
gtacgattgctgcgaaatgattactgtctcctggactttaactaattgtcctcagtttgcgacgatctaggcgaagtcaatcctccgcaaagtggcagaagttcgctaaccatctcaaccgtaagggtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTGAAGCTCAAAGAAGACTATTACGTCATGGATCCCTACAAAGCAGTGGAGC
                     ||||  |   | |  || |       | || ||  |  | || | ||||||||   | |  ||| ||       |||  |  ||| |      ||  ||||  | ||   ||||||| |||||||||||||| || || || ||||| ||||||||  | |||||||||||    || | ||| ||||| ||||| ||| | || || |||||| 
--------------------gtactaacagttcgttttcattcg---gcccccaaatcccaacaagctaggcga---cgaatctcggctctaaaccagtcgcgcgcga------tcgcccgtttgagtcc-tgcagGTTTGCTGGGAGAAGTTCGCGAGGTACTTCGAGGTGGAGCTCAGGGAGGTGAAGCTGCGCGACGGCTACTACGTGATGGACCCCGAGAAGGCGGTGGAGA

upper sequence: PP1S68_116V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G101069_T01 (Zea mays), 3'ss of exon 3
gtacgattgctgcgaaatgattactgtctcctggactttaactaattgtcctcagtttgcgacg-atctaggcgaagtcaatcctccgcaaagtggcagaagttcgctaaccatctcaaccgtaagggtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTGAAGCTCAAAGAAGACTATTACGTCATGGATCCCTACAAAGCAGTGGAGC
                                        ||     ||||   |  ||| |    |||       | | ||   ||      || ||  || |    ||||| |        ||  |    ||||||| |||||||||||||| || || || ||||| ||||||||    |||||||||||||| ||||  || ||||| ||||| ||  | || || | |||| 
--------------------------------------gtacgtccggtccattgcgtgcaaaacgtctgtctactggccatgggccatgcgatgccacgagctgctgaaccacc--------aaacgcgcatgcagGTGTGCTGGGAGAAGTTCGCCAGGTACTTCGAGGTGGAGCTCAAGGAGGTGAAGCTCAAGGAAGGGTACTACGTGATGGACCCAGAGAAGGCCGCGGAGA

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|162186448|gb|FC363004.1|FC363004
EST:     CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAG                         GTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG
genomic: CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAGgtacgattgc ... gtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG
EST: gi|162235796|gb|FC412347.1|FC412347
EST:     CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAG                         GTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG
genomic: CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAGgtacgattgc ... gtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG
EST: gi|67508354|gb|BJ941222.1|BJ941222
EST:     CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAG                         GTCTGCTGGGAGAAG
genomic: CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAGgtacgattgc ... gtttgtgcagGTCTGCTGGGAGAAG
EST: gi|100370735|gb|BY948490.1|BY948490
EST:     CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAG                         GTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG
genomic: CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAGgtacgattgc ... gtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG
EST: gi|100404166|gb|BY955288.1|BY955288
EST:     CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAG                         GTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG
genomic: CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAGgtacgattgc ... gtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG
EST: gi|100371483|gb|BY968001.1|BY968001
EST:     CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAG                         GTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG
genomic: CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAGgtacgattgc ... gtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG
EST: gi|162151020|gb|FC326837.1|FC326837
EST:     CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAG                         GTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG
genomic: CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAGgtacgattgc ... gtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG
EST: gi|100389016|gb|BY952220.1|BY952220
EST:     TGGAAAGCTTTGGGANCA-GCCCAATCTGGTCACGGGTGCAAATGTTCAG                         GTCTGCTGGGAAAAGTTTGCAAGATATTTCGAAATGGAGCTACGCGAAGTT
genomic: TGGAAAGCCTTGGGA-CAAGCCCAATCTGGTCACGGGTGCCAATGTTCAGgtacgattgc ... gtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGT-
EST: gi|67718142|gb|BJ968401.1|BJ968401
EST:     CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAG                         GTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG
genomic: CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAGgtacgattgc ... gtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG
EST: gi|100379799|gb|BY949950.1|BY949950
EST:     TGGAAAGCCTTGGGGACA-GCCCA-TCTGGTCACGGGTGCCA-TGTTCAG                         GTCTGCTGGGAGA-GTTTNGCA-GATATTTCGAAGTGGAGCTACGCGAGGT
genomic: TGGAAAGCCTTGGG-ACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAGgtacgattgc ... gtttgtgcagGTCTGCTGGGAGAAGTTT-GCAAGATATTTCGAAGTGGAGCTACGCGAGGT
EST: gi|100389596|gb|BY952402.1|BY952402
EST:     CTGGAAAGCCTTGGGACA-GCCCAATCTGGTCACGGGTGCCAATGTTCAG                         GTCTGCTGGGAGA
genomic: CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAGgtacgattgc ... gtttgtgcagGTCTGCTGGGAGA
EST: gi|208377786|gb|DC940898.1|DC940898
EST:     CTGGAAAGCCTTGGGACAAGCC-AATCTGGTCACGGGTGCTAATGTTCAG                         GTCTGCTGGGAGAAGTTTGCA
genomic: CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAGgtacgattgc ... gtttgtgcagGTCTGCTGGGAGAAGTTTGCA
EST: gi|100414435|gb|BY992773.1|BY992773
EST:     CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAG                         GTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG
genomic: CTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAGgtacgattgc ... gtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTG

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: 39

GCTTGCTGGTCTCGCATTCAAGAGGAAATGGCAGAACGAGCGGAAAGCAGCTGGAAAGCCTTGGGACAAGCCCAATCTGGTCACGGGTGCCAATGTTCAGgtacgattgc ... gtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTGAAGCTCAAAGAAGACTATTACGTCATGGATCCCTACAAAGCAGTGGAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctccgcaaagtggcagaagttcgctaaccatctcaaccgtaagggtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTGAAGCTCAAAGAAGACTATTACGTCATGGATCCCTACAAAGCAGTGGAGC
                      cgctaac  putative branch site (score: 39)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgattgctgcgaaatgattactgtctcctggactttaactaattgtcctcagtttgcgacgatctaggcgaagtcaatcctccgcaaagtggcagaagttcgctaaccatctcaaccgtaagggtttgtgcagGTCTGCTGGGAGAAGTTTGCAAGATATTTCGAAGTGGAGCTACGCGAGGTGAAGCTCAAAGAAGACTATTACGTCATGGATCCCTACAAAGCAGTGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG