RetrogeneDB ID: retro_trub_33

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_220:443655..444403(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000010639
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NAMPT
• Ensembl ID: ENSTRUG00000016695
• Aliases: None
• Description: None

Sequence

>retro_trub_33
GAGTGCAACTTCAATATATTGCTAGCAACCGATTCAAGGTGGCACAAACAATACCCATCCAACACTAGTAAAGTCTACTC
CTATTTTGAGTACAGGGAGAAGACAAATTCCAGCAACAGCAAAAAGATCAAGTACTATAAAACCGTCTTCTACGGCCTGC
AGTACATCCTGCACAAGTACTTTAAAGGAAAGGTAGTAACTCTAGAAAAGATCCAGGAGGCTAAGAACATTTACAGAGAA
CACTTTCATGATGATGTTTTCAACGAGAAGGGCTGGAGGTACATTTTAGACAAATACAACGGACACCTGCCCATTGAAAT
CAAGGCAGTCCCAGAGGGGATCATTCCTCGGGGCAATGTTTTGTTCACAGTGGAGAGCACAGACCAAAAATGCAACTGGC
TCACCAACTGGGTGGAGACCCTTTGGGTTCAGATCTGGTACCCCATCACTGTCACCACAAACTCCAGAGAGCAGAAGAAG
ATCCTTGCTCGGTACCTTCTGGAGACCTCTGGGAGCTTGGAGGGCCTGGAGTACAAACTGCATGATTTTGGCTACAGGGA
GCTTCTCCTCACAAGAGACTGCAGGTATAGGAGCGTCTGCCCATTTGGTAAATTTCAAGGGAACTGACACAATCGCTGAC
ATTGGAGTCATTAAGAAATTCTACGGGACCAAAGATCCTGTGCCAAGCTTCTCAGTGCCCGCTGCCGAGCACAGTAGCGT
GGGGAAAGAACCACGAAAAGAGGCCTTT

Alignment

ORF - retro_trub_33 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.23 %
• Parental protein coverage: 51.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DADFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKTDPSKSHKVKYDKTVFYGLQYILHKYLKGKVV
          ...FNILLATDS......KQYP.NTSKVYSYFE.REK.T..S.S.K.KY.KTVFYGLQYILHKY.KGKVV
Retrocopy ECNFNILLATDS---RWHKQYPSNTSKVYSYFEYREK-TNSSNSKKIKYYKTVFYGLQYILHKYFKGKVV

Parental  TPEKIQEAKNVYREHFQDDVFNEKGWTYILEKYKGHLPIEIKAVPEGSVIPRGNVLFTVESTDPECYWLT
          T.EKIQEAKN.YREHF.DDVFNEKGW.YIL.KY.GHLPIEIKAVPEG..IPRGNVLFTVESTD..C.WLT
Retrocopy TLEKIQEAKNIYREHFHDDVFNEKGWRYILDKYNGHLPIEIKAVPEG-IIPRGNVLFTVESTDQKCNWLT

Parental  NWVETILVQIWYPITVATNSREQKKILAKYLLETSGSLERLEYKLHDFGYR-GVSSQETAGIGASAHLVN
          NWVET..VQIWYPITV.TNSREQKKILA.YLLETSGSLE.LEYKLHDFGYR...SSQETAGIGASAHLVN
Retrocopy NWVETLWVQIWYPITVTTNSREQKKILARYLLETSGSLEGLEYKLHDFGYR>SFSSQETAGIGASAHLVN

Parental  FKGTDTVAGIGVIKKFYGTKDPVPGFSLPAAEHSTITAWGKDHEKDAF
          FKGTDT.A.IGVIKKFYGTKDPVP.FS.PAAEHS.....GK...K.AF
Retrocopy FKGTDTIADIGVIKKFYGTKDPVPSFSVPAAEHSSV---GKEPRKEAF

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_33 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_33 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_33 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016193	2 retrocopies	retro_cjac_1281, retro_cjac_3877,
Cavia porcellus	ENSCPOG00000009226	1 retrocopy	retro_cpor_848,
Homo sapiens	ENSG00000105835	1 retrocopy	retro_hsap_79,
Oryctolagus cuniculus	ENSOCUG00000013417	1 retrocopy	retro_ocun_777,
Pongo abelii	ENSPPYG00000018270	2 retrocopies	retro_pabe_1407, retro_pabe_1415,
Pan troglodytes	ENSPTRG00000019571	1 retrocopy	retro_ptro_114,
Takifugu rubripes	ENSTRUG00000016695	1 retrocopy	retro_trub_33 ,