RetrogeneDB ID: retro_ptro_648

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:121106113..121106565(-)
• Located in intron of: ENSPTRG00000004405

Retrocopy information

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

Parental gene information

• Parental gene symbol: FUNDC1
• Ensembl ID: ENSPTRG00000021821
• Aliases: None
• Description: None

Sequence

>retro_ptro_648
AACCCGGCTCCCCAAGAATATGAAAGTGAGGACGACTCTTACGAAGTGTTGGATTTAACTGAGTATGCGCGAAGACACCA
GTGGTGGAATCCAGTGTTTGGCCACAGTTCGGGATCTATGGTGGAAAAATACGCAGTAGCTACCCAGATTGTAATGGGTG
GTGTTCCTGGCTGGTTTGCAGGATTTTTGTTCCAGAAAGTTTGAAAACTTGCAGCAACTGCAGTAGGTGGTGACTTTCTT
GCCGTCAGATTGCTAGTCATAGTGGCTACGTGCAGATTAACTGGAAGAGAGTTGAAAAAGATGCAAACAAAGCAAAAAGG
CAGATGAAGAAACGAGCGAACAAAGCAGCACCGGAAATCAACAATTTAATTGAAGAAGCAATAGAATTTATCAAGCAGCA
CATTGTGATACCCGGTAGATTTGTGGGAGGCTTTTTGCTCGGACTTGCATCT

Alignment

ORF - retro_ptro_648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.18 %
• Parental protein coverage: 97.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NPPPQDYESDDDSYEVLDLTEYARRHQWWNRVFGHSSGPMVEKYSVATQIVMGGVTGWCAGFLFQKVGKL
          NP.PQ.YES.DDSYEVLDLTEYARRHQWWN.VFGHSSG.MVEKY.VATQIVMGGV.GW.AGFLFQKV.KL
Retrocopy NPAPQEYESEDDSYEVLDLTEYARRHQWWNPVFGHSSGSMVEKYAVATQIVMGGVPGWFAGFLFQKV*KL

Parental  AATAVGGGFLLL-QIASHSGYVQIDWKRVEKDVNKAKRQIKKRANKAAPEINNLIEEATEFIKQNIVISS
          AATAVGG.FL...QIASHSGYVQI.WKRVEKD.NKAKRQ.KKRANKAAPEINNLIEEA.EFIKQ.IVI..
Retrocopy AATAVGGDFLAV<QIASHSGYVQINWKRVEKDANKAKRQMKKRANKAAPEINNLIEEAIEFIKQHIVIPG

Parental  GFVGGFLLGLAS
          .FVGGFLLGLAS
Retrocopy RFVGGFLLGLAS

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	0.04 RPM	10.08 RPM
SRP007412_cerebellum	0.07 RPM	12.62 RPM
SRP007412_heart	0.00 RPM	13.32 RPM
SRP007412_kidney	0.00 RPM	9.65 RPM
SRP007412_liver	0.00 RPM	4.26 RPM
SRP007412_testis	0.00 RPM	7.27 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_648 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_648 has 0 orthologous retrocopies within eutheria group .

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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,
Pelodiscus sinensis	ENSPSIG00000013793	1 retrocopy	retro_psin_30,
Pan troglodytes	ENSPTRG00000021821	1 retrocopy	retro_ptro_648 ,
Pan troglodytes	ENSPTRG00000041852	4 retrocopies	retro_ptro_1490, retro_ptro_1553, retro_ptro_2254, retro_ptro_2398,
Rattus norvegicus	ENSRNOG00000003470	1 retrocopy	retro_rnor_2644,
Sarcophilus harrisii	ENSSHAG00000000501	1 retrocopy	retro_shar_222,
Tarsius syrichta	ENSTSYG00000009139	1 retrocopy	retro_tsyr_1522,