RetrogeneDB ID: retro_pabe_2474

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:143948369..143948803(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARMC1
• Ensembl ID: ENSPPYG00000018630
• Aliases: None
• Description: armadillo repeat-containing protein 1 [Source:RefSeq peptide;Acc:NP_001125221]

Sequence

>retro_pabe_2474
ATGAATTCTTCCACCTCCACCATGAGTGAAGAGTCTGATACTCTATTGGTAGTTAACCAGTTAGGGGATATAGCAGCCGA
TCCATTAAAGAGAAGAGCTGTCGTCGAGGATCAGGGATGCCTGGCCTTATTTTATTTATGGACCACCCCAACCCTCCAGT
CCATTTGGCTTTGCTTGCTCTTCAATACTTGGGAGAATACCGTGCAAACAGAGAAAAGATGAAAGGAGAACTGGGTATGA
TGTTGAGCCCACAAAATGTTATACAGAAAACTGCAACTCCAGGAGAAACAAAACTTCTGGCCTCTGAAATCTATGACATA
CTTCAGTCCTCCAATAAGGCAGATGGTGATAGTTTCAATGAAAGAAATTAATATTGAAGCAAAGCTCAGTTTTTTCTGGA
AACTACAAACAAACGTGCCAAAACAGTGGTTTTG

Alignment

ORF - retro_pabe_2474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.68 %
• Parental protein coverage: 65.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNSSTSTMSEEPDALSVVNQL-RDLAADPLNRRAIVQDQGCLPGLILFMDHPNPPVVHSALLALRYLAEC
          MNSSTSTMSEE.D.L.VVNQL.R................G..PGLILFMDHPNPPV.H.ALLAL.YL.E.
Retrocopy MNSSTSTMSEESDTLLVVNQL<RGYSSRSIKEKSCRRGSG-MPGLILFMDHPNPPV-HLALLALQYLGEY

Parental  RANREKMKGELGMMLSLQNVIQKTTTPGETKLLASEIYDILQSSNMADGDSFNEMNSRRRKAQFFLGTTN
          RANREKMKGELGMMLS.QNVIQKT.TPGETKLLASEIYDILQSSN.ADGDSFNE.N....KAQFFL.TTN
Retrocopy RANREKMKGELGMMLSPQNVIQKTATPGETKLLASEIYDILQSSNKADGDSFNERN*Y*SKAQFFLETTN

Parental  KRAKTVVL
          KRAKTVVL
Retrocopy KRAKTVVL

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	5.92 RPM
SRP007412_cerebellum	0.12 RPM	6.20 RPM
SRP007412_heart	0.15 RPM	1.72 RPM
SRP007412_kidney	0.07 RPM	1.92 RPM
SRP007412_liver	0.03 RPM	1.84 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2474 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2474 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2474 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015901	1 retrocopy	retro_btau_1447,
Homo sapiens	ENSG00000104442	1 retrocopy	retro_hsap_3100,
Gorilla gorilla	ENSGGOG00000022803	1 retrocopy	retro_ggor_2129,
Myotis lucifugus	ENSMLUG00000014037	1 retrocopy	retro_mluc_2058,
Nomascus leucogenys	ENSNLEG00000003916	1 retrocopy	retro_nleu_1518,
Oryctolagus cuniculus	ENSOCUG00000000392	2 retrocopies	retro_ocun_1437, retro_ocun_782,
Pongo abelii	ENSPPYG00000018630	1 retrocopy	retro_pabe_2474 ,
Pan troglodytes	ENSPTRG00000020298	1 retrocopy	retro_ptro_2096,
Sus scrofa	ENSSSCG00000006220	1 retrocopy	retro_sscr_1027,