RetrogeneDB ID: retro_pabe_806

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:120104126..120104576(-)
• Located in intron of: ENSPPYG00000003988

Retrocopy information

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

Parental gene information

• Parental gene symbol: FUNDC1
• Ensembl ID: ENSPPYG00000020268
• Aliases: None
• Description: FUN14 domain containing 1 [Source:HGNC Symbol;Acc:28746]

Sequence

>retro_pabe_806
AACCCCGCTCCCCAAGAATATGAAAGTGAGGACGACTCTTACGAACTGTTGGATTTAACTGAGTATGCACGAAGGCACCA
GTGGTGGAATCCAGTGTTTGGCCACAGTTCGGGATCTGTGGTGGAAAAATACGCAGTAGCTACCCAGATTGTAATGGGTG
GCGTTCCTGGCTGGTTTGCAGGATTTTTGTTCCAGAAAGTTTGAAAACTTGCAGCAACTGCAGTAGGTGGTGACTTTCTT
GCCGTCAGATTGCTAGTCATAGTGGCTATGTGCAGATTAACTGGAAGAGAGTTGAAAAAGATGTAAACAGCAAAAAGGCA
GATGAAGAAGCGAGCGAACAAAGCAGCACCTGAAATCAACAATTTAATTGAAGAAGCAATAGAATTTATCAAACAGCACA
TTGTGATATCCGGTGGATTTGTGGGAGGCTTTTTTCTCGAACTTGCATCT

Alignment

ORF - retro_pabe_806 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.85 %
• Parental protein coverage: 97.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NPPPQDYESDDDSYEVLDLTEYARRHQWWNRVFGHSSGPMVEKYSVATQIVMGGVTGWCAGFLFQKVGKL
          NP.PQ.YES.DDSYE.LDLTEYARRHQWWN.VFGHSSG..VEKY.VATQIVMGGV.GW.AGFLFQKV.KL
Retrocopy NPAPQEYESEDDSYELLDLTEYARRHQWWNPVFGHSSGSVVEKYAVATQIVMGGVPGWFAGFLFQKV*KL

Parental  AATAVGGGFLLLQIASHSGYVQIDWKRVEKDVNKAKRQIKKRANKAAPEINNLIEEATEFIKQNIVISSG
          AATAVGG.FL...................K....AKRQ.KKRANKAAPEINNLIEEA.EFIKQ.IVIS.G
Retrocopy AATAVGGDFLAVRLLVIVAMCRLTGRELKK-M*TAKRQMKKRANKAAPEINNLIEEAIEFIKQHIVISGG

Parental  FVGGFLLGLAS
          FVGGF.L.LAS
Retrocopy FVGGFFLELAS

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	0.00 RPM	10.89 RPM
SRP007412_cerebellum	0.12 RPM	16.54 RPM
SRP007412_heart	0.00 RPM	7.25 RPM
SRP007412_kidney	0.00 RPM	6.60 RPM
SRP007412_liver	0.00 RPM	4.80 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_806 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_806 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_806 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_936
Gorilla gorilla	retro_ggor_755

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010876	1 retrocopy	retro_cjac_896,
Cavia porcellus	ENSCPOG00000012962	2 retrocopies	retro_cpor_507, retro_cpor_508,
Echinops telfairi	ENSETEG00000012763	3 retrocopies	retro_etel_1614, retro_etel_697, retro_etel_852,
Homo sapiens	ENSG00000069509	1 retrocopy	retro_hsap_936,
Gorilla gorilla	ENSGGOG00000023311	1 retrocopy	retro_ggor_755,
Latimeria chalumnae	ENSLACG00000010215	1 retrocopy	retro_lcha_74,
Macropus eugenii	ENSMEUG00000006795	5 retrocopies	retro_meug_1597, retro_meug_2127, retro_meug_232, retro_meug_415, retro_meug_994,
Microcebus murinus	ENSMICG00000000450	2 retrocopies	retro_mmur_1189, retro_mmur_1461,
Macaca mulatta	ENSMMUG00000003505	1 retrocopy	retro_mmul_38,
Monodelphis domestica	ENSMODG00000021088	3 retrocopies	retro_mdom_1262, retro_mdom_769, retro_mdom_917,
Nomascus leucogenys	ENSNLEG00000002513	2 retrocopies	retro_nleu_2760, retro_nleu_294,
Oryctolagus cuniculus	ENSOCUG00000029753	5 retrocopies	retro_ocun_1008, retro_ocun_1376, retro_ocun_1567, retro_ocun_27, retro_ocun_314,
Pongo abelii	ENSPPYG00000020268	2 retrocopies	retro_pabe_806 , retro_pabe_829,
Pongo abelii	ENSPPYG00000020897	4 retrocopies	retro_pabe_1884, retro_pabe_2646, retro_pabe_2916, retro_pabe_49,
Pelodiscus sinensis	ENSPSIG00000013793	1 retrocopy	retro_psin_30,
Pan troglodytes	ENSPTRG00000021821	1 retrocopy	retro_ptro_648,
Rattus norvegicus	ENSRNOG00000003470	1 retrocopy	retro_rnor_2644,
Sarcophilus harrisii	ENSSHAG00000000501	1 retrocopy	retro_shar_222,
Tarsius syrichta	ENSTSYG00000009139	1 retrocopy	retro_tsyr_1522,