RetrogeneDB ID: retro_pabe_2480

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:158672501..158673260(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: FAM192A
• Ensembl ID: ENSPPYG00000007382
• Aliases: None
• Description: family with sequence similarity 192, member A [Source:HGNC Symbol;Acc:29856]

Sequence

>retro_pabe_2480
ATGGATGGAGGGGATGATCATAACCTTGTTATCAAAAAGAGCTTTGTGTCTGAGGCAGAACTAGATGAATGGTGCAAAAG
GAGGCAAGAAGAATGGGAGAAAGTTTGAAAACCTGAAGATCCAGAAGAATGTCCAGAGGAGGTTTATGACCCTCGATCTC
TATATGAAAGGCTACAGGAACAGAAGGACAGGAAGCAGCAGGAGTATAAGGAACAGTTCAAATTCAAAAACATGGTAAGA
GGCTTAGATGAAGATGAGACCAACTTCCTTGATGAGGTTTCTCGACAGCAGGAACTAATAGAAAAGCAACAAAGAGAAGA
AGAACTGAAAGAACTGAAGGAATACAGAAATAACCTCAAGAAGGCTGAAATTTCTCAAGAGAACAAGAAGGAAGTGGAAA
AGAAACTGACTGTGAAGCCCATAGAAACCAAGAATAAGTTCTCCCAGGCAAAGCTGTTGGCAGGAGCTGTGAAACATAAG
AGCTCAGAGAGTGACAACAGTGTGAAAAGACTGAAACCGGACCCTGAGCCAGATGACAAGAATCAAGAGCCCTCATCCTG
CAAGTCTCTGGGAAATACCTCCCTGAGTGTCCCCTCCATCCACTGCCCCTCTGCTGCAGTCTGTATCAGCATCCTCCCAG
GCCTGGCCTCCTCTGGGAGCAGCGACTCTGAGTCCAGCTCAGACAGTAAAGGCACCACCAATGCCACCGGAAAGATCATC
TCCTCCATCTTCCAAACCAACACTTTCCTCGAGTCCCCC

Alignment

ORF - retro_pabe_2480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDGGDDGNLVIKKRFVSEAELDERRKRRQEEWEKVRKPEDPEECPEEVYDPRSLYERLQEQKDRKQQEYE
          MDGGDD.NLVIKK.FVSEAELDE..KRRQEEWEKV.KPEDPEECPEEVYDPRSLYERLQEQKDRKQQEY.
Retrocopy MDGGDDHNLVIKKSFVSEAELDEWCKRRQEEWEKV*KPEDPEECPEEVYDPRSLYERLQEQKDRKQQEYK

Parental  EQFKFKNMVRGLDEDETNFLDEVSRQQELIEKQRREEELKELKEYRNNLKKVGISQENKKEVEKKLTVKP
          EQFKFKNMVRGLDEDETNFLDEVSRQQELIEKQ.REEELKELKEYRNNLKK..ISQENKKEVEKKLTVKP
Retrocopy EQFKFKNMVRGLDEDETNFLDEVSRQQELIEKQQREEELKELKEYRNNLKKAEISQENKKEVEKKLTVKP

Parental  IETKNKFSQAKLLAGAVKHKSSESGNSVKRLKPDPEPDDKNQEPSSCKSLGNTSLSGPSIHCPSAAVCIG
          IETKNKFSQAKLLAGAVKHKSSES.NSVKRLKPDPEPDDKNQEPSSCKSLGNTSLS.PSIHCPSAAVCI.
Retrocopy IETKNKFSQAKLLAGAVKHKSSESDNSVKRLKPDPEPDDKNQEPSSCKSLGNTSLSVPSIHCPSAAVCIS

Parental  ILPGLGAYSGSSDSESSSDSEGTINATGKIVSSIFRTNTFLEAP
          ILPGL.A.SGSSDSESSSDS.GT.NATGKI.SSIF.TNTFLE.P
Retrocopy ILPGL-ASSGSSDSESSSDSKGTTNATGKIISSIFQTNTFLESP

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.17 RPM	36.71 RPM
SRP007412_cerebellum	2.31 RPM	35.63 RPM
SRP007412_heart	0.30 RPM	13.43 RPM
SRP007412_kidney	0.63 RPM	29.27 RPM
SRP007412_liver	0.43 RPM	18.58 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2480 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2480 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2480 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2994
Pan troglodytes	retro_ptro_2025
Gorilla gorilla	retro_ggor_2074

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002242	1 retrocopy	retro_btau_1133,
Cavia porcellus	ENSCPOG00000001392	1 retrocopy	retro_cpor_122,
Equus caballus	ENSECAG00000009324	1 retrocopy	retro_ecab_710,
Echinops telfairi	ENSETEG00000014379	1 retrocopy	retro_etel_930,
Homo sapiens	ENSG00000172775	1 retrocopy	retro_hsap_2994,
Gorilla gorilla	ENSGGOG00000003938	1 retrocopy	retro_ggor_2074,
Macaca mulatta	ENSMMUG00000013492	1 retrocopy	retro_mmul_189,
Mus musculus	ENSMUSG00000031774	1 retrocopy	retro_mmus_428,
Nomascus leucogenys	ENSNLEG00000002716	1 retrocopy	retro_nleu_745,
Ochotona princeps	ENSOPRG00000006909	2 retrocopies	retro_opri_175, retro_opri_579,
Pongo abelii	ENSPPYG00000007382	1 retrocopy	retro_pabe_2480 ,
Pan troglodytes	ENSPTRG00000008148	1 retrocopy	retro_ptro_2025,
Tarsius syrichta	ENSTSYG00000013300	1 retrocopy	retro_tsyr_884,
Tursiops truncatus	ENSTTRG00000012791	1 retrocopy	retro_ttru_1884,
Vicugna pacos	ENSVPAG00000005973	1 retrocopy	retro_vpac_321,