RetrogeneDB ID: retro_pabe_2093

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:134239215..134239668(+)
• Located in intron of: ENSPPYG00000013354

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCTD2
• Ensembl ID: ENSPPYG00000008616
• Aliases: None
• Description: potassium channel tetramerization domain containing 2 [Source:HGNC Symbol;Acc:21294]

Sequence

>retro_pabe_2093
AAGGATGAAACTGTTGCCTATTTAATGGACAGAGACCCCACCTATTTTGGGCCTGTGCTGAACTACCTGAGACATGGCAA
GCTGGTGATTAACAAAGACCTTGTGGAGGAAGGAGTGTTGGAAAAAGCAGAATTTTACAGTATCACTTCATTAATAAAAC
TTGTAAAGGACAAAATTAGAGAACAAGAGAGCAAAACATCACAGGTGCCCATGAAGCATGTGTACCGCGTGCTTCAGTGT
CAGGAGGAGAAACTCACACAGGTGGTGTCCACCATGTCCGACAGCTGGAAGTTTGAACAACTGGTCAGCAATGGCTCCTC
TTACAACTATGGGAATGAAGATCAGGCCAGGTTCCTCTATGTGGTGTCCAAGGAACTTCACAACACCCTGTACAGTACGG
CCAGTGAACCCAGCAAGAAGGCCAAGATTTTGTAAGAACAAGGTTCAAGGATG

Alignment

ORF - retro_pabe_2093 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.19 %
• Parental protein coverage: 81.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QDETGAYLIDRDPTYFGPILNYLRHGKLIITKELAEEGVLEEAEFYNIASLVRLVKERIRDNENRTSQGP
          .DET.AYL.DRDPTYFGP.LNYLRHGKL.I.K.L.EEGVLE.AEFY.I.SL..LVK..IR..E..TSQ.P
Retrocopy KDETVAYLMDRDPTYFGPVLNYLRHGKLVINKDLVEEGVLEKAEFYSITSLIKLVKDKIREQESKTSQVP

Parental  VKHVYRVLQCQEEELTQMVSTMSDGWKFEQLISIGSSYNYGNEDQAEFLQVVSRELNNSTNGIVIEPS-E
          .KHVYRVLQCQEE.LTQ.VSTMSD.WKFEQL.S.GSSYNYGNEDQA.FL.VVS.EL.N.......EPS..
Retrocopy MKHVYRVLQCQEEKLTQVVSTMSDSWKFEQLVSNGSSYNYGNEDQARFLYVVSKELHNTLYSTASEPSKK

Parental  ARILQERGSRM
          A.IL.E.GSRM
Retrocopy AKIL*EQGSRM

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	0.11 RPM	21.95 RPM
SRP007412_cerebellum	0.36 RPM	29.43 RPM
SRP007412_heart	0.03 RPM	2.23 RPM
SRP007412_kidney	0.03 RPM	6.60 RPM
SRP007412_liver	0.06 RPM	1.16 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2093 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2093 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2224
Pan troglodytes	retro_ptro_1685
Gorilla gorilla	retro_ggor_1752

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021231	1 retrocopy	retro_btau_927,
Callithrix jacchus	ENSCJAG00000014605	1 retrocopy	retro_cjac_2781,
Echinops telfairi	ENSETEG00000013965	1 retrocopy	retro_etel_643,
Pongo abelii	ENSPPYG00000008616	1 retrocopy	retro_pabe_2093 ,
Pongo abelii	ENSPPYG00000018452	3 retrocopies	retro_pabe_1527, retro_pabe_2725, retro_pabe_3457,
Pan troglodytes	ENSPTRG00000009629	1 retrocopy	retro_ptro_1685,