Sequence
atgc intronic sequence ATGC exonic sequencegttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccagatacaaatttaaatagtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccgtagGTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCT
Basic information
species | Physcomitrella patens |
transcript | PP1S168_104V6.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os05g41930.1 (Oryza sativa), 3'ss of exon 4
gttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccagatacaaatttaaatagtaggtagaacatttg--ttaagtcactgcttatccactcaatttttatttgaccgtagGTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCT
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----------------------------gtaatggtt-acagctggc-----gtgtgtttatttctcattta---cttttggtttcatgcactgatattctgct--atattcattctac--tagGTGAGGATCCGCATTAGAAAGCTCTGCAAGCCTTTGGAAGAGGATGCTTTCAGACCAGTGCTGCACCATTACGATGGTCCAAAGTTTCGTCTTGAGCTCT
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G033117_T01 (Zea mays), 3'ss of exon 4
gttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccagatacaaatttaaatagtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccg---tagGTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCT
| | | ||| || | || || | | || | | | | ||| || ||| |||||| ||| | ||| | |||| ||| ||||| || |||||||| || ||||||||||| |||| || ||||||||||| |||||||| ||| ||||||
-------------------------------------------gtactggtaacatcatttgtcattacgttcattcctcatttccttttgattccttgctctgacgtttccttcaccatgttagGTGAGGATCTGCATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCATTATGATGGGCCAAAGTTCCGCCTTGAGCTCT
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA08G02840.1 (Glycine max), 3'ss of exon 3
gttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccagatacaaatttaaatagtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccgtagGTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCT
||| ||| | | ||| || | || | | | | | | | | | || | | | | | || || | | || | |||| || | | | || ||| | || | || ||||| || ||||||||| | || || ||||||||||| ||||||||||||||| ||||
-------------------tagtgtaaaaattttgtacactaattaattg-tatcggtatgatttat-gatttattacttcgtggatgatgcttaagatgcttcataaatgat-gattgcagGTACGAGTGATAACTAGGAAAACTTGTGAACCACTGGAGGAGGATTCCTTCAGGCCAATCCTTCACCACTATGATGGTCCCAAGTTCCGTCTTGAGCTGA
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA05G36700.1 (Glycine max), 3'ss of exon 3
gttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccagatacaaatttaaatagtaggtagaacat-ttgttaagtcactgcttatc-cactcaatttttatttgaccgtagGTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCT
||||| |||| | | | || | | || | ||| | | || | || |||||| || || | | || | |||| || | | | || ||| | || | || || || || ||||||||| | || || ||||||||||| ||||||||||||||| ||||
----------------------tgttagtgtaaaattcttt-tacactaattaatggtatcggtatgaagtatgatttattactttgtgggtgcttaagatgcttcataaatgat-gattgcagGTACGAGTGATAACTAGGAAAACTTGTGAACCACTGGAGGAAGATTCCTTCAGGCCAATCCTTCACCACTATGATGGTCCCAAGTTCCGTCTTGAGCTGA
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA16G06100.1 (Glycine max), 3'ss of exon 4
gttgaatctcaaagcattgcgatgttaaatagt---gattcacggtttgccagatacaaatttaaatagtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccgtagGTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCT
| | | || | |||| | | | || ||| || | ||| | ||| | || | ||| || | || | | | || || |||||| | | ||| | | |||| || ||| | || ||||| || || ||||||||||| ||||||| ||||||||||| ||||| |||||| |||| |
-------------gtagtagaatatagaatattttgaaatggtgggagaccatgtatgagcttatct-----gtaaatcaatgaataaaacaatatttttgttccttctcttcctt-----gtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTCAGGCCAGTATTGCATCATTATGATGGGCCAAAGTTTCGTCTTGAGCTGT
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G27090.1 (Arabidopsis thaliana), 3'ss of exon 4
gttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccagatacaaatttaaatagtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccgtagGTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCT
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-----------------------gtgaaact-taaatcacaat--gactttcattgttttaagtctttattttgatatcttgta--ctaata--taacttctttctcttaaattg-taacagGTAAGGATCAGAGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTCAGGCCAGTACTTCACCACTATGATGGTCCAAAATTCCGCCTTGAGCTCT
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv02s0025g01720.t01 (Vitis vinifera), 3'ss of exon 3
gttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccagatacaaatttaaatagtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccgtagGTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCT
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---------------gaagaaattccccatacccatctgcttaat-ctagatgatggtccatttaataaa-aggtcat--actgaattggggttta-ccattctgtggttttgtga--atagGTGCGGGTGGTCACCAGGAAAATCTGTGAGCCAATGGAAGAGGATTCATTCAGGCCGGTCCTCCATCACTATGACGGCCCCAAGTTCCGCCTGGAGCTGAMapped 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|22132955|gb|BQ827456.1|BQ827456EST: CCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG GTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTT
genomic: CCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAGgttgaatctc ... ttgaccgtagGTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccgtagGTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCT
atttgac putative branch site (score: 4)
tttttattt CT-rich tract
actcaatttttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccagatacaaatttaaatagtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccgtagGTGCGGACTCGTATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC