RetrogeneDB ID: retro_pabe_1759

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1_random:15273513..15274332(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT8
• Ensembl ID: ENSPPYG00000011318
• Aliases: None
• Description: None

Sequence

>retro_pabe_1759
TCCTCTTCAGTATTGCATGGCATTGATTTTTAAGGAAGAACCAAAAGTGATGTACATCTGTCAAAGATGCAAAAATAGCA
GTGTACTCTTGTCCTTTTGATGGCATGATAACAGAAACTAAGGGAACAGTGTTGATAAAGACTGATGAAGAATTGATGAA
CTTTAGTAAGGGAGAAGAAAATCTCATGGATGCATAAGTCAAAGCTATTGCTGATACTGGTGCAAATGTCATAGTAACAG
GTGGCAAAGTGGCAGACATGGCTCTTCATTATGCAAACAAATATAATATCACGTTAGTGAGGCTAAACTCAAAATGGGAT
CTCCGAAGACTCTGTAAAACAGTTGGTGGCTACAGCTCTTCCTAGATTGACACCTCCTGTCCTTGAAGAAATGGGACACT
GTGACAGTGTTTACCTCTCAGAAGTTGGAGATACTCAGATGGTGGTTTTTAAGCATGAAAAGGAAGATGGTACCATTTCT
ACCATAGTACTTCGAGGCTCTACAGACAATCTGATGGATGACATAGAAAGGGCAGTAGATGATGGTGTTAATACTTTCAA
AGTTCTTACAAGGGATAAATGTCTTGTACCCGGAGGTGGAGCAACAGAAATTGAATTAGCCAAACAGATCACATCATATG
GACAGACATGTCCTGGACTTGAACAGTATGCTATTAAGAAGTTTGCTGAGGCGTTTGAAGCTATTCCCTGTGCACTGGCG
GAAAATTCTGGAGTTAAGGCCAGTGAAGTAATCTCTAAACTTTATGCAGTACATCAAGAAGGAAATAAAAATGTTGGATT
AGATACTGAGGCTGAAGTC

Alignment

ORF - retro_pabe_1759 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.36 %
• Parental protein coverage: 50.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSSVLHGMVFKKETEGDV-TSVKDAKIAVYSCPFDGMITETKGTVLIKTAEELMNFSKGEENLMDAQVKA
          SSSVLHG..F...T..DV.TSVKDAKIAVYSCPFDGMITETKGTVLIKT.EELMNFSKGEENLMDA.VKA
Retrocopy SSSVLHGIDF*GRTKSDV<TSVKDAKIAVYSCPFDGMITETKGTVLIKTDEELMNFSKGEENLMDA*VKA

Parental  IADTGANVVVTGGKVADMALHYANKYNIMLVRLNSKWDLRRLCKTVG-ATALPRLTPPVLE-MGHCDSVY
          IADTGANV.VTGGKVADMALHYANKYNI.LVRLNSKWDLRRLCKTVG.ATALPRLTPPVLE.MGHCDSVY
Retrocopy IADTGANVIVTGGKVADMALHYANKYNITLVRLNSKWDLRRLCKTVG>ATALPRLTPPVLEEMGHCDSVY

Parental  LSEVGDTQVVVFKHEKEDGAISTIVLRGSTDNLMDDIERAVDDGVNTFKVLTRDKRLVPGGGATEIELAK
          LSEVGDTQ.VVFKHEKEDG.ISTIVLRGSTDNLMDDIERAVDDGVNTFKVLTRDK.LVPGGGATEIELAK
Retrocopy LSEVGDTQMVVFKHEKEDGTISTIVLRGSTDNLMDDIERAVDDGVNTFKVLTRDKCLVPGGGATEIELAK

Parental  QITSYGETCPGLEQYAIKKFAEAFEAIPRALAENSGVKANEVISKLYAVHQEGNKNVGLDIEAEV
          QITSYG.TCPGLEQYAIKKFAEAFEAIP.ALAENSGVKA.EVISKLYAVHQEGNKNVGLD.EAEV
Retrocopy QITSYGQTCPGLEQYAIKKFAEAFEAIPCALAENSGVKASEVISKLYAVHQEGNKNVGLDTEAEV

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	65.91 RPM
SRP007412_cerebellum	0.24 RPM	78.19 RPM
SRP007412_heart	0.00 RPM	49.73 RPM
SRP007412_kidney	0.03 RPM	50.62 RPM
SRP007412_liver	0.58 RPM	45.11 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1759 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1759 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1759 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000156261	1 retrocopy	retro_hsap_449,
Gorilla gorilla	ENSGGOG00000006344	1 retrocopy	retro_ggor_435,
Pongo abelii	ENSPPYG00000011318	1 retrocopy	retro_pabe_1759 ,