RetrogeneDB ID: retro_pabe_443

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:129082318..129082719(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf123
• Ensembl ID: ENSPPYG00000001336
• Aliases: None
• Description: chromosome 1 open reading frame 123 [Source:HGNC Symbol;Acc:26059]

Sequence

>retro_pabe_443
CAGTGGTACCTGAAAATGAAATGTGGCAATGGTAGTGAGATTTCAGAGAAGTGGCACTACATCCAACTGATGGACAGTGT
GGCACTAAAGTGGGGCCATGGCAGCTCCTTCATGGTCCAGAAGTGCAAGCTGTGCACACAGGAAACTCCACTGAGGTTTT
CAATGGCAGCATCAAATCTTACAATGCCAAAGACAGAGAGAAGTTCAAAACTATTATAGAGTTTGAGTGCCAGGGCTTCC
AACCATTTGATTTCCAGCCCTAGGCTGGGTTTTCTGCTGAGGGCACAAAGTCAAAGACAGTCTTTGGTGACATTCTGCAG
GAGAAAGACTGGACTGACTATGACAAAAAGTCCAGGGAGTCTGTGGGAATCTCTGAGGTCATTCAGCAGTTTTTGAAATG
C

Alignment

ORF - retro_pabe_443 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.65 %
• Parental protein coverage: 72.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RWYLKMKCGNCGEISDKWQYIRLMDSMALKGGRGSASMVQKCKLCARE-NSIEILSSTIKPYNAEDNENF
          .WYLKMKCGN..EIS.KW.YI.LMDS.ALK.G.GS..MVQKCKLC..E.NS.E.....IK.YNA.D.E.F
Retrocopy QWYLKMKCGNGSEISEKWHYIQLMDSVALKWGHGSSFMVQKCKLCTQE<NSTEVFNGSIKSYNAKDREKF

Parental  KTIVEFECRGLEPVDFQPQAGFAAEGVESGTAFSDINLQEKDWTDYDEKAQESVGIYEVTHQFVKC
          KTI.EFEC.G..P.DFQP.AGF.AEG..S.T.F.DI.LQEKDWTDYD.K..ESVGI.EV..QF.KC
Retrocopy KTIIEFECQGFQPFDFQP*AGFSAEGTKSKTVFGDI-LQEKDWTDYDKKSRESVGISEVIQQFLKC

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	6.58 RPM
SRP007412_cerebellum	0.00 RPM	6.32 RPM
SRP007412_heart	0.12 RPM	3.79 RPM
SRP007412_kidney	0.00 RPM	5.77 RPM
SRP007412_liver	0.00 RPM	5.54 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_443 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_443 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_443 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_192
Gorilla gorilla	retro_ggor_271

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004526	3 retrocopies	retro_cjac_2948, retro_cjac_3149, retro_cjac_3186,
Cavia porcellus	ENSCPOG00000011509	1 retrocopy	retro_cpor_1142,
Homo sapiens	ENSG00000162384	1 retrocopy	retro_hsap_192,
Gorilla gorilla	ENSGGOG00000004027	1 retrocopy	retro_ggor_271,
Microcebus murinus	ENSMICG00000006397	1 retrocopy	retro_mmur_1113,
Myotis lucifugus	ENSMLUG00000002439	1 retrocopy	retro_mluc_101,
Mus musculus	ENSMUSG00000028608	1 retrocopy	retro_mmus_975,
Nomascus leucogenys	ENSNLEG00000017988	1 retrocopy	retro_nleu_1001,
Oryctolagus cuniculus	ENSOCUG00000029317	1 retrocopy	retro_ocun_770,
Otolemur garnettii	ENSOGAG00000013324	1 retrocopy	retro_ogar_861,
Ochotona princeps	ENSOPRG00000009003	2 retrocopies	retro_opri_351, retro_opri_711,
Pongo abelii	ENSPPYG00000001336	1 retrocopy	retro_pabe_443 ,
Pan troglodytes	ENSPTRG00000000752	1 retrocopy	retro_ptro_99,
Rattus norvegicus	ENSRNOG00000012724	3 retrocopies	retro_rnor_1999, retro_rnor_2403, retro_rnor_2705,