RetrogeneDB ID: retro_pabe_1553

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:23505542..23505865(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOMM20
• Ensembl ID: ENSPPYG00000000099
• Aliases: None
• Description: Mitochondrial import receptor subunit TOM20 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q5RA31]

Sequence

>retro_pabe_1553
CTGGGCCAGAACAGTGCCGTCATAGCCAGGGTACGCAGGGCCCTTTTCATTGGGTACTGCATTTACTTAGACCACAAGAG
ACGGAGTGACCCTAACTTCAAGAACAGGCTGTGAGAACAAAGAAAGAAACAGAAGCTTGCCAAGGAGAGAGCTAAGCTTT
GCAAGTGACCTGACCTTAAAGTTGCTGAAGCTGTTCAGAAATCTTCTTTGAAGAAATACAGCTCAGAGAAGAGTTACTAG
CTCAAGGTGAGTGTGAGAAGGACATGGAGCATCTGATGACAGGGAGTGCTGGATGTGGACAGTTACTGCAAGTGTCCAGT
GTT

Alignment

ORF - retro_pabe_1553 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.72 %
• Parental protein coverage: 74.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VGRNSAIAAGVCGALFIGYCIYFDRKRRSDPNFKNRLRERRKKQKLAKERAGLSKLPDLKDAEAVQK-FF
          .G.NSA..A.V..ALFIGYCIY.D.KRRSDPNFKNRL.E.RKKQKLAKERA.L.K.PDLK.AEAVQK..F
Retrocopy LGQNSAVIARVRRALFIGYCIYLDHKRRSDPNFKNRL*EQRKKQKLAKERAKLCK*PDLKVAEAVQK<IF

Parental  LEEIQLGEELLAQGEYEKGVDHLTNAIAVCGQPQQLLQV
          .EEIQL.EELLAQGE.EK...HL....A.CGQ..Q...V
Retrocopy FEEIQLREELLAQGECEKDMEHLMTGSAGCGQLLQVSSV

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	14.71 RPM
SRP007412_cerebellum	0.00 RPM	7.66 RPM
SRP007412_heart	0.00 RPM	3.82 RPM
SRP007412_kidney	0.00 RPM	9.94 RPM
SRP007412_liver	0.00 RPM	9.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1553 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1553 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1553 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1906
Pan troglodytes	retro_ptro_1252
Gorilla gorilla	retro_ggor_1395

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 97 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000562	5 retrocopies	retro_btau_1025, retro_btau_1147, retro_btau_1357, retro_btau_492, retro_btau_533,
Choloepus hoffmanni	ENSCHOG00000002383	7 retrocopies	retro_chof_1381, retro_chof_1699, retro_chof_2252, retro_chof_2497, retro_chof_2511, retro_chof_415, retro_chof_901,
Callithrix jacchus	ENSCJAG00000018127	3 retrocopies	retro_cjac_1860, retro_cjac_2420, retro_cjac_918,
Echinops telfairi	ENSETEG00000017693	4 retrocopies	retro_etel_1224, retro_etel_130, retro_etel_1514, retro_etel_559,
Homo sapiens	ENSG00000173726	5 retrocopies	retro_hsap_1827, retro_hsap_1906, retro_hsap_3866, retro_hsap_4702, retro_hsap_796,
Gorilla gorilla	ENSGGOG00000025184	5 retrocopies	retro_ggor_1395, retro_ggor_2166, retro_ggor_2606, retro_ggor_2923, retro_ggor_656,
Loxodonta africana	ENSLAFG00000015499	1 retrocopy	retro_lafr_436,
Myotis lucifugus	ENSMLUG00000016218	1 retrocopy	retro_mluc_644,
Macaca mulatta	ENSMMUG00000007136	2 retrocopies	retro_mmul_1255, retro_mmul_273,
Monodelphis domestica	ENSMODG00000008452	6 retrocopies	retro_mdom_1112, retro_mdom_1172, retro_mdom_1297, retro_mdom_1527, retro_mdom_1568, retro_mdom_838,
Mus musculus	ENSMUSG00000093904	12 retrocopies	retro_mmus_1437, retro_mmus_1669, retro_mmus_1698, retro_mmus_1990, retro_mmus_2026, retro_mmus_2141, retro_mmus_3142, retro_mmus_3311, retro_mmus_3637, retro_mmus_3655, retro_mmus_457, retro_mmus_935,
Pongo abelii	ENSPPYG00000000099	4 retrocopies	retro_pabe_1497, retro_pabe_1553 , retro_pabe_3650, retro_pabe_708,
Pan troglodytes	ENSPTRG00000002127	5 retrocopies	retro_ptro_1166, retro_ptro_1252, retro_ptro_2634, retro_ptro_3124, retro_ptro_554,
Rattus norvegicus	ENSRNOG00000019980	4 retrocopies	retro_rnor_1191, retro_rnor_1958, retro_rnor_1983, retro_rnor_2103,
Sarcophilus harrisii	ENSSHAG00000015876	3 retrocopies	retro_shar_272, retro_shar_512, retro_shar_669,
Ictidomys tridecemlineatus	ENSSTOG00000027564	3 retrocopies	retro_itri_248, retro_itri_71, retro_itri_820,
Tupaia belangeri	ENSTBEG00000003827	26 retrocopies	retro_tbel_1483, retro_tbel_2215, retro_tbel_2239, retro_tbel_2240, retro_tbel_2340, retro_tbel_2348, retro_tbel_2440, retro_tbel_2472, retro_tbel_2548, retro_tbel_2610, retro_tbel_2619, retro_tbel_3000, retro_tbel_3182, retro_tbel_3204, retro_tbel_3674, retro_tbel_3687, retro_tbel_3729, retro_tbel_3808, retro_tbel_3895, retro_tbel_3949, retro_tbel_4068, retro_tbel_4096, retro_tbel_4136, retro_tbel_4596, retro_tbel_4625, retro_tbel_600,
Vicugna pacos	ENSVPAG00000003980	1 retrocopy	retro_vpac_252,