RetrogeneDB ID: retro_trub_36

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_253:251645..252382(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000008416
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PITPNB
• Ensembl ID: ENSTRUG00000018546
• Aliases: None
• Description: None

Sequence

>retro_trub_36
TCGGTGGCTGAAGGCAGCAAGAAGGAGACAGGCGGAGGAGAGGGCATCGAGGTTCTGAAGAACGAACCGTACGAGGGGGA
AAGCGAAAAAGGACAGTACACCCACAAATCTATCATCTAAAGAGTAAAGTCTCAGCATTTATAAAGCTGATTGCACCAGA
GGGATCATTAGCTTTTCACGAGAAGGCCTGGAACGCCTACCCCTACTGCCGCACTATTGTGACCAACGGGTACATGAAGG
ATGACATTGTGATAAAGATCAAGACGTGGCACAAGCCCGACATGGGAGCATTAGAAAATGTTCATCAGCTGGACGAGGAG
ACCCTAAAGGGTGTGGAAGTGGTCTCTTTAGATATTGCAAACAAAGACGAAGAGGCTCCAGGCGACTACAAACCAGAGGA
AGAGCCTGCTCTGCTCCAGTCCACTAAAACGGGCAGAGGACCTCTAAGTCCTGAGTGGAAGGACGAGCTGAGGTCGGAAT
GTCCTCAAATGTGCACATACAAACTGGTCACAGTCCAATTCCACTGGTGGGGTCTGCAGACCAAAGTGGAGAACTTCATC
CACAAGCAAGAAAAGCGTATTTTCACAAACTTTCACCGCCAACTCTTCTGCTGGATGGACAGATGGGTGGGTTTGAGCAT
GGAGGACATCAGGCAGATGGAAGATGAGACCCAAAAGGAGCTCGAGGAGCTGCGTAATAAAGGTCCAGTTCGAGGCACCA
CTGCCGCTCATGAGCAA

Alignment

ORF - retro_trub_36 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 91.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVAEASKNETGGGEGIEVLKNEPYEKEGEKGQYTHK-IYHLKSKVPGFVKMIAPEGSLVFHEKAWNAYPY
          SVAE.SK.ETGGGEGIEVLKNEPYE.E.EKGQYTHK.IYHLKSKV..F.K.IAPEGSL.FHEKAWNAYPY
Retrocopy SVAEGSKKETGGGEGIEVLKNEPYEGESEKGQYTHK<IYHLKSKVSAFIKLIAPEGSLAFHEKAWNAYPY

Parental  CRTIVTNEYMKDDFMIKIETWHKPDMGTLENVHQLDEQTLKDVEVVPIDIANKDEVAPGDYKPEEDPALF
          CRTIVTN.YMKDD..IKI.TWHKPDMG.LENVHQLDE.TLK.VEVV..DIANKDE.APGDYKPEE.PAL.
Retrocopy CRTIVTNGYMKDDIVIKIKTWHKPDMGALENVHQLDEETLKGVEVVSLDIANKDEEAPGDYKPEEEPALL

Parental  HSAKTGRGPLSPEWKNELKSECPHMCAYKLVTVKFRWWGLQTKVENIIHKQEKRIFTNFHRQLFCWIDKW
          .S.KTGRGPLSPEWK.EL.SECP.MC.YKLVTV.F.WWGLQTKVEN.IHKQEKRIFTNFHRQLFCW.D.W
Retrocopy QSTKTGRGPLSPEWKDELRSECPQMCTYKLVTVQFHWWGLQTKVENFIHKQEKRIFTNFHRQLFCWMDRW

Parental  VGLTMEDIRRMEDETQRELEELRSKGPVRGTSAAHEQ
          VGL.MEDIR.MEDETQ.ELEELR.KGPVRGT.AAHEQ
Retrocopy VGLSMEDIRQMEDETQKELEELRNKGPVRGTTAAHEQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Takifugu rubripes was not studied using RNA-Seq expression data.

ChIP-Seq

Takifugu rubripes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_trub_36 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_36 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_36 has 0 orthologous retrocopies within teleost group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012309	2 retrocopies	retro_chof_2374, retro_chof_860,
Cavia porcellus	ENSCPOG00000012298	1 retrocopy	retro_cpor_957,
Macropus eugenii	ENSMEUG00000010442	3 retrocopies	retro_meug_392, retro_meug_689, retro_meug_786,
Oryctolagus cuniculus	ENSOCUG00000000511	1 retrocopy	retro_ocun_1620,
Otolemur garnettii	ENSOGAG00000000391	1 retrocopy	retro_ogar_1300,
Ochotona princeps	ENSOPRG00000002540	1 retrocopy	retro_opri_931,
Tupaia belangeri	ENSTBEG00000000293	1 retrocopy	retro_tbel_4285,
Takifugu rubripes	ENSTRUG00000018546	1 retrocopy	retro_trub_36 ,
Tarsius syrichta	ENSTSYG00000001148	1 retrocopy	retro_tsyr_503,
Tursiops truncatus	ENSTTRG00000001278	2 retrocopies	retro_ttru_1060, retro_ttru_1439,