RetrogeneDB ID: retro_pabe_643

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10_random:25165568..25166200(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000002808
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM213A
• Ensembl ID: ENSPPYG00000025862
• Aliases: None
• Description: family with sequence similarity 213, member A [Source:HGNC Symbol;Acc:28651]

Sequence

>retro_pabe_643
CTTGAGGACCCAAGTTTCTTCACCATGGGGATGTGGTCCATTGGTGCAGGAGCCTTGGGGGCTGCTGCCTTGGCATTGCT
GCTTGCCAACACAGACGTGTTTCTGTCCAAGCCCCAGAAAGCGGCCCTGGAGTACCTGGAGGATATAGACCTGAAAACAC
TGCAGAAGGAACCAAGGACTTTGAAAGCAAAGGAGCTATGCGGAAAAAATGGAGCTGTGATTATGGCAGTGCGGAGGCCA
GGCTGTTTCCTCTGTCGAGAGGAAGCTGCGGATCTGTCCTCCCTGAAAAGCATGTTGGACCAGCTGGGCGTCCCCTTCTA
TGCAGTAGTAAAGGAGCACATCAGGACCGAAGTGAAGGATTTCCAGCCTTATTTCAAAAGAGAAATCTTCCTGGATGAAA
AAAAAAGTTCTATGGTCCACAAAGGCGGAAGATGATGTTTACGGGATTTATCCGTCTGGGAGTGTGGTACAACTTCTTCC
GAGCCTGGAATGGAGTCTTCTCTGGAAACCTGGAAGGAGAAGGCTTCATCCTTGGGGGAGTTTTCGTGGTGGGATCAGGA
AAGCAGGGCATTCTTCTTGGGCACCGAGAAAATGAATCTGGAGACAAGGTAAACCTGCTTTCTGTTCTGGAA

Alignment

ORF - retro_pabe_643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.98 %
• Parental protein coverage: 92.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQDPSFFTMGMWSIGAGALGAAALALLLAKTDVFLSKPQKAALEYLEDIDLKTLEKEPRTLKAKELWEKN
          L.DPSFFTMGMWSIGAGALGAAALALLLA.TDVFLSKPQKAALEYLEDIDLKTL.KEPRTLKAKEL..KN
Retrocopy LEDPSFFTMGMWSIGAGALGAAALALLLANTDVFLSKPQKAALEYLEDIDLKTLQKEPRTLKAKELCGKN

Parental  GAVIMAVRRPGCFLCREEAADLSSLKSMLDQLGVPLYAVVKEHIRTEVKDFQPYFKGEIFLD-EKKKFYG
          GAVIMAVRRPGCFLCREEAADLSSLKSMLDQLGVP.YAVVKEHIRTEVKDFQPYFK.EIFLD.....FYG
Retrocopy GAVIMAVRRPGCFLCREEAADLSSLKSMLDQLGVPFYAVVKEHIRTEVKDFQPYFKREIFLD<XXXXFYG

Parental  PQRRKMMFMGFIRLGVWYNFFRAWNGGFSGNLEGEGFILGGVFVVGSGKQGILLEHREKEFGDKVNLLSV
          PQRRKMMF.GFIRLGVWYNFFRAWNG.FSGNLEGEGFILGGVFVVGSGKQGILL.HRE.E.GDKVNLLSV
Retrocopy PQRRKMMFTGFIRLGVWYNFFRAWNGVFSGNLEGEGFILGGVFVVGSGKQGILLGHRENESGDKVNLLSV

Parental  LE
          LE
Retrocopy LE

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	36.66 RPM
SRP007412_cerebellum	0.00 RPM	8.63 RPM
SRP007412_heart	0.03 RPM	7.62 RPM
SRP007412_kidney	0.03 RPM	21.48 RPM
SRP007412_liver	0.00 RPM	15.52 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_643 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_643 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_643 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000813	1 retrocopy	retro_chof_878,
Callithrix jacchus	ENSCJAG00000003657	1 retrocopy	retro_cjac_3312,
Dasypus novemcinctus	ENSDNOG00000001981	3 retrocopies	retro_dnov_1843, retro_dnov_1901, retro_dnov_868,
Homo sapiens	ENSG00000122378	2 retrocopies	retro_hsap_1135, retro_hsap_4076,
Gorilla gorilla	ENSGGOG00000013246	2 retrocopies	retro_ggor_2733, retro_ggor_886,
Microcebus murinus	ENSMICG00000007485	2 retrocopies	retro_mmur_1346, retro_mmur_1481,
Macaca mulatta	ENSMMUG00000021773	3 retrocopies	retro_mmul_2351, retro_mmul_2409, retro_mmul_881,
Mus musculus	ENSMUSG00000021792	1 retrocopy	retro_mmus_2227,
Otolemur garnettii	ENSOGAG00000013638	7 retrocopies	retro_ogar_2126, retro_ogar_2435, retro_ogar_2562, retro_ogar_3327, retro_ogar_420, retro_ogar_580, retro_ogar_784,
Procavia capensis	ENSPCAG00000009696	1 retrocopy	retro_pcap_281,
Pongo abelii	ENSPPYG00000025862	4 retrocopies	retro_pabe_3345, retro_pabe_643 , retro_pabe_738, retro_pabe_944,
Pan troglodytes	ENSPTRG00000002685	2 retrocopies	retro_ptro_2763, retro_ptro_774,
Rattus norvegicus	ENSRNOG00000011140	1 retrocopy	retro_rnor_1517,