RetrogeneDB ID: retro_pabe_496

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:214861596..214862040(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHCHD2
• Ensembl ID: ENSPPYG00000017543
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain containing 2 [Source:HGNC Symbol;Acc:21645]

Sequence

>retro_pabe_496
GGAAGCCGAAGCCACACCTCCCGCATGGCCCCTCCGGCCAGCCGGGCCCCTCAGATGAGAGCTGCACTCAGGCCAGCACC
AGTCGCTCAGCCACCAGCAGCGGCACCCCCATCTGCAGTTGGCTCTTCTGCTGCTGTGCCCCGGCAGCCAGGTCTGATGG
CCCAGATGGCAACCACTGCAGCTGACGTGGCTGTGGGCTCTGCTGTGGGGCACACACTGGGTCATGCCATTACTGGGGGC
TTCAGTGGAGGAAGTAATGCTGAGCCTGCGAGGCCTCTCATCACTTACCAGGATCCTCAGGGAACCCAGCCGGCACAGCA
GCAGCAGCCTTGCTTCTATGAGATCAAACAGTTTCTGGAGTGTGCCCAGAAGCAGGGTGACATCAAGCTCTGTGAGGGTT
TCAGTGAGATGCTGAAACAGTGCCGACTTGCAAACGGATTGGCC

Alignment

ORF - retro_pabe_496 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.24 %
• Parental protein coverage: 98.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSRSRTSRMAPPASRAPQMRAAPRPAPVAQPPAAAPPSAVGSSAAAPWQPGLMAQMATTAAGVAVGSAVG
          GSRS.TSRMAPPASRAPQMRAA.RPAPVAQPPAAAPPSAVGSSAA.P.QPGLMAQMATTAA.VAVGSAVG
Retrocopy GSRSHTSRMAPPASRAPQMRAALRPAPVAQPPAAAPPSAVGSSAAVPRQPGLMAQMATTAADVAVGSAVG

Parental  HTLGHAITGGFSGGSNAEPARPDITYQEPQGTQPSQQQQPCFYEIKQFLECAQNQGDIKLCEGFSEVLKQ
          HTLGHAITGGFSGGSNAEPARP.ITYQ.PQGTQP.QQQQPCFYEIKQFLECAQ.QGDIKLCEGFSE.LKQ
Retrocopy HTLGHAITGGFSGGSNAEPARPLITYQDPQGTQPAQQQQPCFYEIKQFLECAQKQGDIKLCEGFSEMLKQ

Parental  CRLANGLA
          CRLANGLA
Retrocopy CRLANGLA

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	52.53 RPM
SRP007412_cerebellum	0.00 RPM	57.03 RPM
SRP007412_heart	0.00 RPM	51.75 RPM
SRP007412_kidney	0.00 RPM	69.41 RPM
SRP007412_liver	0.00 RPM	54.99 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_496 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_496 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_496 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016050	2 retrocopies	retro_amel_500, retro_amel_976,
Bos taurus	ENSBTAG00000040295	2 retrocopies	retro_btau_397, retro_btau_768,
Canis familiaris	ENSCAFG00000010178	1 retrocopy	retro_cfam_1653,
Callithrix jacchus	ENSCJAG00000021267	1 retrocopy	retro_cjac_271,
Erinaceus europaeus	ENSEEUG00000012857	1 retrocopy	retro_eeur_398,
Echinops telfairi	ENSETEG00000008598	1 retrocopy	retro_etel_45,
Homo sapiens	ENSG00000106153	8 retrocopies	retro_hsap_116, retro_hsap_1180, retro_hsap_1995, retro_hsap_3063, retro_hsap_3186, retro_hsap_4057, retro_hsap_4184, retro_hsap_4752,
Gorilla gorilla	ENSGGOG00000014938	8 retrocopies	retro_ggor_2103, retro_ggor_220, retro_ggor_2725, retro_ggor_2807, retro_ggor_2808, retro_ggor_2958, retro_ggor_918, retro_ggor_989,
Myotis lucifugus	ENSMLUG00000015151	1 retrocopy	retro_mluc_345,
Mus musculus	ENSMUSG00000070493	2 retrocopies	retro_mmus_2340, retro_mmus_2536,
Nomascus leucogenys	ENSNLEG00000015819	6 retrocopies	retro_nleu_1250, retro_nleu_1657, retro_nleu_2096, retro_nleu_2108, retro_nleu_555, retro_nleu_770,
Otolemur garnettii	ENSOGAG00000010097	5 retrocopies	retro_ogar_1161, retro_ogar_158, retro_ogar_1848, retro_ogar_2837, retro_ogar_34,
Pongo abelii	ENSPPYG00000017543	4 retrocopies	retro_pabe_131, retro_pabe_139, retro_pabe_1755, retro_pabe_496 ,
Pan troglodytes	ENSPTRG00000019209	9 retrocopies	retro_ptro_129, retro_ptro_1331, retro_ptro_2065, retro_ptro_2259, retro_ptro_2750, retro_ptro_2838, retro_ptro_3046, retro_ptro_3167, retro_ptro_809,
Sus scrofa	ENSSSCG00000007743	1 retrocopy	retro_sscr_515,
Ictidomys tridecemlineatus	ENSSTOG00000010512	3 retrocopies	retro_itri_1870, retro_itri_670, retro_itri_671,
Tupaia belangeri	ENSTBEG00000012905	15 retrocopies	retro_tbel_1728, retro_tbel_1891, retro_tbel_2513, retro_tbel_2593, retro_tbel_2596, retro_tbel_2658, retro_tbel_3331, retro_tbel_3764, retro_tbel_3777, retro_tbel_3954, retro_tbel_4082, retro_tbel_4368, retro_tbel_4487, retro_tbel_4728, retro_tbel_817,
Tursiops truncatus	ENSTTRG00000015185	1 retrocopy	retro_ttru_520,
Vicugna pacos	ENSVPAG00000006104	1 retrocopy	retro_vpac_48,