RetrogeneDB ID: retro_pabe_2924

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:158379350..158379850(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000004215
• Aliases: None
• Description: None

Sequence

>retro_pabe_2924
ATGGCCACACTCAGTGTTGGAGTCCAACCTTGTGACCGGAATGATGGGGAGCAGGAACAGAACTTGGATGCTATGGCACC
CAAGAGGCCCTGACCTGGGGCAGGAAACAGGTTTGGAGGCCATAGGCTCCTTGTGGTGCTGGAGGAGGCCAGTCTGGAGA
CAGTCCAGGTAGGGAATACATAAGAGCTGCTCAGCTGTGACAAGCGCAAGTCTATGTTGTTGAAGAATGGACGTGACCCT
GGGGAGGAGCGCTCAGACACAGCCCAGCAGAGTGCCCTGACACTGCTGGAGAGTCTCCTGAGCCAAGCTGGCGTGCTGCA
GGTTTCTACCCACACGCAGAAGAAGGTTCTGATTGAAGTGAGCCCGCAGACCTGAATTCCCAGAACCTTTGACCACTTTT
GTGGCCTCATGGTTCAGCTTTTACACAAGCTCAGTGTTGGAGCAGCTGATGGCCCCCAGAAGCTCTTGAAGGTAAATAAG
AATCAGTGTCAGATCACTTT

Alignment

ORF - retro_pabe_2924 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.24 %
• Parental protein coverage: 68.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAPSGGFKPRERSGGEQAQDWDAVPPKRPRLGAGNKIGGRRLIVVLEGASLETVKVGKTYELLNCDKHK
          MA..S.G..P..R..GEQ.Q..DA..PKRP..GAGN..GG.RL.VVLE.ASLETV.VG.T.ELL.CDK.K
Retrocopy MATLSVGVQPCDRNDGEQEQNLDAMAPKRP*PGAGNRFGGHRLLVVLEEASLETVQVGNT*ELLSCDKRK

Parental  SILLKNGRDPGEVRPDITHQSLLMLMDSPLNRAGLLQVYIHTQKNVLIEVNPQTRIPRTFDRFCGLMVQL
          S.LLKNGRDPGE.R.D...QS.L.L..S.L..AG.LQV..HTQK.VLIEV.PQT.IPRTFD.FCGLMVQL
Retrocopy SMLLKNGRDPGEERSDTAQQSALTLLESLLSQAGVLQVSTHTQKKVLIEVSPQT*IPRTFDHFCGLMVQL

Parental  LHKLSVRAADGPQKLLKVIKN-PVSDHF
          LHKLSV.AADGPQKLLKV.KN..VSDHF
Retrocopy LHKLSVGAADGPQKLLKVNKN<SVSDHF

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	15.92 RPM
SRP007412_cerebellum	0.00 RPM	10.82 RPM
SRP007412_heart	0.00 RPM	14.39 RPM
SRP007412_kidney	0.00 RPM	23.04 RPM
SRP007412_liver	0.00 RPM	18.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2924 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2924 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2924 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013753	1 retrocopy	retro_amel_1924,
Callithrix jacchus	ENSCJAG00000007120	1 retrocopy	retro_cjac_2960,
Gorilla gorilla	ENSGGOG00000004287	1 retrocopy	retro_ggor_3077,
Macropus eugenii	ENSMEUG00000000831	1 retrocopy	retro_meug_1299,
Myotis lucifugus	ENSMLUG00000009196	1 retrocopy	retro_mluc_737,
Macaca mulatta	ENSMMUG00000010207	1 retrocopy	retro_mmul_671,
Nomascus leucogenys	ENSNLEG00000005080	1 retrocopy	retro_nleu_501,
Otolemur garnettii	ENSOGAG00000006975	2 retrocopies	retro_ogar_2971, retro_ogar_945,
Pongo abelii	ENSPPYG00000004215	1 retrocopy	retro_pabe_2924 ,
Rattus norvegicus	ENSRNOG00000012828	1 retrocopy	retro_rnor_1459,