RetrogeneDB ID: retro_pabe_1119

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:60855044..60855402(+)
• Located in intron of: ENSPPYG00000005870

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCOC
• Ensembl ID: ENSPPYG00000015077
• Aliases: None
• Description: short coiled-coil protein [Source:HGNC Symbol;Acc:20335]

Sequence

>retro_pabe_1119
GTCCAAGTGTCCAGCCTGAGGCATCCTCCCCATCCCTTCCTCTCCCAGCACCTCAAACATTCATCATTCATCAAGGATTT
TGTATCCAAGGCCTAAAAGTTTGTTACCCAAGATGACAAATATTGACATGGATGCAGTTGATGCTGAAAATCATTTGGAA
TTGGAGGGAAAAACACAGCTTATTAATCAAGTGTTGGAACTCCAACATACACTTGAAGATCTCCCTGTCAGAGGAGATGC
AGTTACGGAAGAAAATCTCAAACTAAAATCAGAAAACCAAGTTCTTGGACAATACACAGAAAATTTCATGTCAGCTTCTA
GTGTTTTTCAAACAACTGACACAAAAAGCAAAAGAAAA

Alignment

ORF - retro_pabe_1119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.15 %
• Parental protein coverage: 75.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VQVSRL-EVSAGSLPLLTPQAE-DHSSRILYPRPKSLLPKMMNADMDAVDAENQVELEEKTRLINQVLEL
          VQVS.L.E.S..SLPL..PQ....HSSRILYPRPKSLLPKM.N.DMDAVDAEN..ELE.KT.LINQVLEL
Retrocopy VQVSSL<EASSPSLPLPAPQTF<HHSSRILYPRPKSLLPKMTNIDMDAVDAENHLELEGKTQLINQVLEL

Parental  QHTLEDLSARVDAVKEENLKLKSENQVLGQYIENLMSASSVFQTTDTKSKRK
          QHTLEDL..R.DAV.EENLKLKSENQVLGQY.EN.MSASSVFQTTDTKSKRK
Retrocopy QHTLEDLPVRGDAVTEENLKLKSENQVLGQYTENFMSASSVFQTTDTKSKRK

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	44.67 RPM
SRP007412_cerebellum	0.00 RPM	69.31 RPM
SRP007412_heart	0.00 RPM	33.99 RPM
SRP007412_kidney	0.00 RPM	24.89 RPM
SRP007412_liver	0.00 RPM	13.13 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1119 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1119 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1119 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1347
Pan troglodytes	retro_ptro_922
Gorilla gorilla	retro_ggor_1048
Macaca mulatta	retro_mmul_2186
Callithrix jacchus	retro_cjac_713

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 62 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010957	2 retrocopies	retro_amel_176, retro_amel_725,
Bos taurus	ENSBTAG00000022109	2 retrocopies	retro_btau_1843, retro_btau_1847,
Canis familiaris	ENSCAFG00000003699	2 retrocopies	retro_cfam_1564, retro_cfam_667,
Choloepus hoffmanni	ENSCHOG00000000604	10 retrocopies	retro_chof_1154, retro_chof_1651, retro_chof_1973, retro_chof_1980, retro_chof_2214, retro_chof_2394, retro_chof_2595, retro_chof_289, retro_chof_563, retro_chof_862,
Callithrix jacchus	ENSCJAG00000003060	2 retrocopies	retro_cjac_713, retro_cjac_95,
Dipodomys ordii	ENSDORG00000000177	8 retrocopies	retro_dord_359, retro_dord_461, retro_dord_476, retro_dord_578, retro_dord_634, retro_dord_639, retro_dord_712, retro_dord_724,
Erinaceus europaeus	ENSEEUG00000011107	1 retrocopy	retro_eeur_19,
Homo sapiens	ENSG00000153130	2 retrocopies	retro_hsap_1347, retro_hsap_228,
Gorilla gorilla	ENSGGOG00000028186	2 retrocopies	retro_ggor_1048, retro_ggor_291,
Macropus eugenii	ENSMEUG00000014534	2 retrocopies	retro_meug_1580, retro_meug_823,
Macaca mulatta	ENSMMUG00000022351	1 retrocopy	retro_mmul_2186,
Monodelphis domestica	ENSMODG00000025528	2 retrocopies	retro_mdom_1163, retro_mdom_1265,
Mustela putorius furo	ENSMPUG00000016119	2 retrocopies	retro_mputfur_468, retro_mputfur_708,
Nomascus leucogenys	ENSNLEG00000005081	2 retrocopies	retro_nleu_1830, retro_nleu_849,
Oryctolagus cuniculus	ENSOCUG00000006591	3 retrocopies	retro_ocun_1400, retro_ocun_1657, retro_ocun_429,
Otolemur garnettii	ENSOGAG00000026414	2 retrocopies	retro_ogar_2489, retro_ogar_3043,
Procavia capensis	ENSPCAG00000003165	2 retrocopies	retro_pcap_119, retro_pcap_457,
Pongo abelii	ENSPPYG00000015077	2 retrocopies	retro_pabe_1119 , retro_pabe_423,
Pan troglodytes	ENSPTRG00000016460	2 retrocopies	retro_ptro_198, retro_ptro_922,
Sarcophilus harrisii	ENSSHAG00000003474	1 retrocopy	retro_shar_572,
Ictidomys tridecemlineatus	ENSSTOG00000028529	3 retrocopies	retro_itri_1170, retro_itri_357, retro_itri_451,
Tarsius syrichta	ENSTSYG00000011814	6 retrocopies	retro_tsyr_1232, retro_tsyr_1446, retro_tsyr_1566, retro_tsyr_2025, retro_tsyr_34, retro_tsyr_446,
Tursiops truncatus	ENSTTRG00000010677	1 retrocopy	retro_ttru_123,