RetrogeneDB ID: retro_pabe_418

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:95670010..95670851(-)
• Located in intron of: ENSPPYG00000000739

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000025918
• Aliases: None
• Description: None

Sequence

>retro_pabe_418
GACCTGGTGGTGCAGAAGGTGGTGGTCCACCCCCAGGCACTGCTCCATGTGGTGGATCATTTCAATAGAATCAGCAAGGT
TGGAAACCAGAAATGCATTCTTCATGTGCTTTTGTGGTCATGGCAAATGAAAGTACTTGATGTATCCAGCAGTTTTACAG
TCCCTTTTAATGAAGATGACAAAGATAATTGTTTTTTAGGCCACGATTATTTGGAAAACATGTACAGAATGTTTAAGAGG
GTGAATGCCAGGGAAAGAATAGTTGAATGGTACCACATAGGCCCTAAACTACACAAGAATGACACTGCCTTCAATGAAAT
CATGAAAAGATACTGCCATAACTCAGTATTGGTCACTAGTGACATGAAGCCAAAGGACTTTAGGGCTGCCTACAGAAGCA
TATATTTCAGTAGAAGTCTACGATGATGGAACTTCAGCCTTGAAAACATTTGAGCATGTGACCAGTGAAACTGGAGCAGA
GGAAGCTAAGGAAATTGGAGTTAAACACTTGTTACATGACATCAAAGACACTACAGTGGGCACTCTTTCCCAATGTATCA
CAAACCAGGTCCTGGATTTGAAGGGACTGAACTCCAAGCTTCTGGGTACCAGAAGCTACCTGGAAAAAGCTGCCACAGGC
AAACTGTCCACCAACCACCAATTCATCTATCAGCTGCAGGTCTTCAAGCTGCTGCCAGTCATCGGCCTATAGGAGTTTGT
CAAGGCCTTTTACCTGAAGACCAATAACCAAATGGTAGCAGTATACCTGGCCTCGCCGATCCATTCTGGGATCACCCTAC
ACAACCTCATCAACAAGAGTGCCAACTGGGATGCAGAGAAG

Alignment

ORF - retro_pabe_418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.57 %
• Parental protein coverage: 87.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELAVQKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDSVWFLDH
          .L.VQKVVVHP..LL.VVDHFNRI.KVGNQK....VLL.SWQ.KVLDVS.SF.VPF.EDDKD....FL.H
Retrocopy DLVVQKVVVHPQALLHVVDHFNRISKVGNQKCILHVLLWSWQMKVLDVSSSFTVPFNEDDKDNC--FLGH

Parental  DYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSVLVIIDVKPKD-LGLPTEAYISV
          DYLENMY.MFK.VNARERIV.WYH.GPKLHKND.A.NE.MKRYC.NSVLV..D.KPKD.LGLPTEAYISV
Retrocopy DYLENMYRMFKRVNARERIVEWYHIGPKLHKNDTAFNEIMKRYCHNSVLVTSDMKPKD>LGLPTEAYISV

Parental  EEVHDDGTPTSKTFEHVTSEIGAEEAEEVGVEHLLRDIKDTTVGTLSQRITNQVHGLKGLNSKLLDIRSY
          E.V.DDGT...KTFEHVTSE.GAEEA.E.GV.HLL.DIKDTTVGTLSQ.ITNQV..LKGLNSKLL..RSY
Retrocopy E-VYDDGTSALKTFEHVTSETGAEEAKEIGVKHLLHDIKDTTVGTLSQCITNQVLDLKGLNSKLLGTRSY

Parental  LEKVATGKLPINHQIIYQLQDVFNLLPDVSLQEFVKAFYLKTNDQMVVVYLASLIRSVVALHNLINNKIA
          LEK.ATGKL..NHQ.IYQLQ.VF.LLP...L.EFVKAFYLKTN.QMV.VYLAS.I.S...LHNLI.NK.A
Retrocopy LEKAATGKLSTNHQFIYQLQ-VFKLLPVIGL*EFVKAFYLKTNNQMVAVYLASPIHSGITLHNLI-NKSA

Parental  NRDAEK
          N.DAEK
Retrocopy NWDAEK

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	0.06 RPM	14.26 RPM
SRP007412_cerebellum	0.12 RPM	8.51 RPM
SRP007412_heart	0.09 RPM	9.24 RPM
SRP007412_kidney	0.13 RPM	7.62 RPM
SRP007412_liver	0.09 RPM	8.72 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_418 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_418 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_418 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_234
Pan troglodytes	retro_ptro_205
Macaca mulatta	retro_mmul_417

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015129	2 retrocopies	retro_cjac_1520, retro_cjac_2910,
Homo sapiens	ENSG00000103035	2 retrocopies	retro_hsap_1781, retro_hsap_234,
Gorilla gorilla	ENSGGOG00000009774	1 retrocopy	retro_ggor_2235,
Myotis lucifugus	ENSMLUG00000005416	1 retrocopy	retro_mluc_505,
Macaca mulatta	ENSMMUG00000011125	4 retrocopies	retro_mmul_1242, retro_mmul_372, retro_mmul_417, retro_mmul_566,
Nomascus leucogenys	ENSNLEG00000005608	1 retrocopy	retro_nleu_1310,
Otolemur garnettii	ENSOGAG00000014868	1 retrocopy	retro_ogar_388,
Procavia capensis	ENSPCAG00000014356	1 retrocopy	retro_pcap_399,
Pongo abelii	ENSPPYG00000003512	1 retrocopy	retro_pabe_175,
Pongo abelii	ENSPPYG00000025918	1 retrocopy	retro_pabe_418 ,
Pan troglodytes	ENSPTRG00000008343	2 retrocopies	retro_ptro_1192, retro_ptro_205,
Ictidomys tridecemlineatus	ENSSTOG00000013123	1 retrocopy	retro_itri_1665,
Tupaia belangeri	ENSTBEG00000016950	1 retrocopy	retro_tbel_4135,