RetrogeneDB ID: retro_pabe_559

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:108866776..108867534(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PHB2
• Ensembl ID: ENSPPYG00000004214
• Aliases: None
• Description: prohibitin-2 [Source:RefSeq peptide;Acc:NP_001125603]

Sequence

>retro_pabe_559
GCCATCTTCTTCAATTATATCGCTGGCATGCAGCAGGACACTATCCTGGCCAAAGGCTTCATTTCAGGATTCCCTGGTCT
CGGTACCCCATCAACGATGACATTCTGGCCAGACCTTGAAAAATTTCCTCCCTAACAGGCTCAAAAGACCTGCAGATGGC
GAACATATCCCTGTACACGGTGTCTCAACCCAGTGTTCAGGAGCTTCCTAGCATGCACAAGCACCTAGGGCTAGACAACA
AAGAATGAGTGTTGCCATCCATTGTCAAAAGAGTATTCAATATTGTGTTGGCCAAGTTCAATGCCTCATAGCTGATTACC
CAGTGGGCCCAGGTATCCCTGTTGATTCATTGGGAGCTGCCACAGAGGGCCAAGGACTTCAATCTTATCTTGGATGATGT
AGCCATCACAGAGTTTGAGCTTTAGCTGAGAGTACACAGCTACTGTAGAGGCCAAAAAGCGGGTCCAACAGGAGGCTCAT
CAGGCCCAGTTCTTGGTAGAAAAGCAAAACTATAACATCAGCAAAGAATGCTCAGGCCAAGTGTGAAGCCAGTCTGCTAA
GATGCTTGGGGAAGCACTGAACAAGAATCCTGGCTACATCAAATTTACAAAGATTAAGCAGCCCAAAAAATCCTCCAAGA
ACAATCAAATCACAAAATCAAATCTGGTCTCACTTGATGAAAAATCTTGTGTTGAACCTTACAGGATAAAATTTTCACCC
TGGGGAAAAAGAAAGCAGCCCTTCTTAAAGGGTAAAAA

Alignment

ORF - retro_pabe_559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.52 %
• Parental protein coverage: 83.95 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  AIFFNRIGGVQQDTILAEG-LHFRIPWFQYPIIYDIRARPRKISSPTGSKDLQMVNISLRVLSRPNAQEL
          AIFFN.I.G.QQDTILA.G.LHFRIPW..YPI..DI.ARP.KISS.TGSKDLQM.NISL...S.P..QEL
Retrocopy AIFFNYIAGMQQDTILAKG<LHFRIPWSRYPINDDILARP*KISSLTGSKDLQMANISLYTVSQPSVQEL

Parental  PSMYQRLGLDYEERVLPSIVNEVLKSVVAKFNASQLITQRAQVSLLIRRELTERAKDFSLILDDVAITE-
          PSM...LGLD..E.VLPSIV..V...V.AKFNAS.LITQ.AQVSLLI..EL..RAKDF.LILDDVAITE.
Retrocopy PSMHKHLGLDNKE*VLPSIVKRVFNIVLAKFNAS*LITQWAQVSLLIHWELPQRAKDFNLILDDVAITE>

Parental  LSFSREYTAAVEAKQVAQQEAQRAQFLVE-KAKQEQRQKIV-QAEGEA-EAAKMLGEALSKNPGYIKLRK
          LSFS.EYTA.VEAK...QQEA..AQFLVE.KAK....Q....QA..EA...AKMLGEAL.KNPGYIK..K
Retrocopy LSFS*EYTATVEAKKRVQQEAHQAQFLVE<KAKL*HQQRML<QAKCEA<QSAKMLGEALNKNPGYIKFTK

Parental  IRAAQNISK-TIATSQNRIYL-TADNLVLN-LQDESFTRGSD--SLIKGKK
          I......SK.TI..SQN.I......NLVLN.LQD..FT.G.....L.KG.K
Retrocopy IKQPKKSSK>TI-KSQNQIWSHLMKNLVLN>LQDKIFTLGKKKAALLKG*K

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	44.73 RPM
SRP007412_cerebellum	0.00 RPM	40.25 RPM
SRP007412_heart	0.00 RPM	40.49 RPM
SRP007412_kidney	0.00 RPM	85.25 RPM
SRP007412_liver	0.00 RPM	86.79 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_559 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_559 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_559 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013760	1 retrocopy	retro_amel_1928,
Canis familiaris	ENSCAFG00000014439	1 retrocopy	retro_cfam_1885,
Callithrix jacchus	ENSCJAG00000007137	1 retrocopy	retro_cjac_781,
Homo sapiens	ENSG00000215021	1 retrocopy	retro_hsap_624,
Gorilla gorilla	ENSGGOG00000004281	1 retrocopy	retro_ggor_547,
Macaca mulatta	ENSMMUG00000010205	2 retrocopies	retro_mmul_2599, retro_mmul_2623,
Nomascus leucogenys	ENSNLEG00000005021	2 retrocopies	retro_nleu_121, retro_nleu_450,
Pongo abelii	ENSPPYG00000004214	3 retrocopies	retro_pabe_419, retro_pabe_557, retro_pabe_559 ,
Rattus norvegicus	ENSRNOG00000012999	1 retrocopy	retro_rnor_2373,