RetrogeneDB ID: retro_pabe_2092

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:127839866..127840157(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC167
• Ensembl ID: ENSPPYG00000016563
• Aliases: None
• Description: coiled-coil domain containing 167 [Source:HGNC Symbol;Acc:21239]

Sequence

>retro_pabe_2092
ATGACTAAAAAAAAGCGGGAGAATCTGGGCGTCGCTCTAGAGATCATTGGGCTAGAGGAGAAGCTGTCCCAGTGTCGGAG
AGACCTGGAGGCCGTGAACTCCAGGCTCCACAGCCGGGAGCTGAGCCCAGAGGCCAGGAGGTCCCTGGAGAAGGAGAAAA
ACAGCCTAATGAACAAAGCTTCCAACTATGAGAAGGAACTGAAGTTTCTTCGGCAAGAGAACTGGAAGAACATGCTGCTC
TCTGTGGCCATCTTTTTCCTCCTGACGCTCATCTATGCCTACTGGACCATG

Alignment

ORF - retro_pabe_2092 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTKKKRENLGVALEIDGLEEKLSQCRRDLEAVNSRLHSRELSPEARRSLEKEKNSLMNKASNYEKELKFL
          MT...RENLGVALEI.GLEEKLSQCRRDLEAVNSRLHSRELSPEARRSLEKEKNSLMNKASNYEKELKFL
Retrocopy MTXXXRENLGVALEIIGLEEKLSQCRRDLEAVNSRLHSRELSPEARRSLEKEKNSLMNKASNYEKELKFL

Parental  RQENRKNMLLSVAIFFLLTLVYAYWTM
          RQEN.KNMLLSVAIFFLLTL.YAYWTM
Retrocopy RQENWKNMLLSVAIFFLLTLIYAYWTM

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	5.42 RPM
SRP007412_cerebellum	0.00 RPM	4.38 RPM
SRP007412_heart	0.00 RPM	2.80 RPM
SRP007412_kidney	0.00 RPM	6.17 RPM
SRP007412_liver	0.03 RPM	8.54 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2092 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2092 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2092 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012069	2 retrocopies	retro_btau_30, retro_btau_517,
Canis familiaris	ENSCAFG00000030835	1 retrocopy	retro_cfam_1854,
Callithrix jacchus	ENSCJAG00000005622	2 retrocopies	retro_cjac_3293, retro_cjac_960,
Felis catus	ENSFCAG00000006745	1 retrocopy	retro_fcat_1558,
Mus musculus	ENSMUSG00000024018	1 retrocopy	retro_mmus_3487,
Otolemur garnettii	ENSOGAG00000000921	1 retrocopy	retro_ogar_880,
Pongo abelii	ENSPPYG00000016563	1 retrocopy	retro_pabe_2092 ,