RetrogeneDB ID: retro_pabe_276

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:96564184..96564467(+)
• Located in intron of: ENSPPYG00000000772

Retrocopy information

• Ensembl ID: ENSPPYG00000000773
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GOLGA7
• Ensembl ID: ENSPPYG00000018542
• Aliases: None
• Description: golgin A7 [Source:HGNC Symbol;Acc:24876]

Sequence

>retro_pabe_276
GGCACACGCTGCCAGTTCCCAGACCAAGTTCCCCCATGGAGCTGGAGAACCCAGATTNGATAGGCAGCAGTTTGAAGAAA
TAGTTCAGAACTCTAAATAACATTTATGCAGAAGCAGAGAAGCTTGTGTGGCCAATCATATCTCGAAGGTTGTTTGGCTT
GTTTAACTGCATATACCATCTTCCTATGCTTGGAAACTCATTACCAGAAGGTTCTGAAGAAAGTCTCCAAATGCATTCAA
GGGCAGAATGAGAAGATCTATGCTCCACAAAGGCCTTCTTCTG

Alignment

ORF - retro_pabe_276 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.47 %
• Parental protein coverage: 67.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GTRCQF-QTKFPAEL-ENRIDRQQFEETV-RTLNNLYAEAEKLG-GQSYLEGCLACLTAYTIFLCMETHY
          GTRCQF.QTKFP....E.R.DRQQFEE.V.RTLNN.YAEAEKL..GQSYLEGCLACLTAYTIFLC.ETHY
Retrocopy GTRCQF>QTKFPHGAGEPRXDRQQFEEIV>RTLNNIYAEAEKLV>GQSYLEGCLACLTAYTIFLCLETHY

Parental  EKVLKKVSKYIQEQNEKIYAPQ-GLLL
          .KVLKKVSK.IQ.QNEKIYAPQ.GLLL
Retrocopy QKVLKKVSKCIQGQNEKIYAPQ>GLLL

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	22.39 RPM
SRP007412_cerebellum	0.00 RPM	37.21 RPM
SRP007412_heart	0.00 RPM	9.69 RPM
SRP007412_kidney	0.00 RPM	26.19 RPM
SRP007412_liver	0.00 RPM	20.87 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_276 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_276 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_276 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002741	1 retrocopy	retro_amel_1785,
Dasypus novemcinctus	ENSDNOG00000009976	2 retrocopies	retro_dnov_194, retro_dnov_45,
Erinaceus europaeus	ENSEEUG00000013699	1 retrocopy	retro_eeur_588,
Felis catus	ENSFCAG00000018740	3 retrocopies	retro_fcat_1209, retro_fcat_1958, retro_fcat_975,
Homo sapiens	ENSG00000147533	1 retrocopy	retro_hsap_3862,
Loxodonta africana	ENSLAFG00000009146	1 retrocopy	retro_lafr_273,
Microcebus murinus	ENSMICG00000000940	1 retrocopy	retro_mmur_721,
Myotis lucifugus	ENSMLUG00000014516	2 retrocopies	retro_mluc_1348, retro_mluc_787,
Monodelphis domestica	ENSMODG00000010474	2 retrocopies	retro_mdom_1034, retro_mdom_1528,
Mus musculus	ENSMUSG00000015341	3 retrocopies	retro_mmus_2687, retro_mmus_312, retro_mmus_3572,
Nomascus leucogenys	ENSNLEG00000012577	1 retrocopy	retro_nleu_3014,
Oryctolagus cuniculus	ENSOCUG00000007546	1 retrocopy	retro_ocun_1503,
Otolemur garnettii	ENSOGAG00000003707	2 retrocopies	retro_ogar_2968, retro_ogar_3484,
Pongo abelii	ENSPPYG00000018542	1 retrocopy	retro_pabe_276 ,
Pan troglodytes	ENSPTRG00000020193	1 retrocopy	retro_ptro_2632,
Rattus norvegicus	ENSRNOG00000017956	1 retrocopy	retro_rnor_2793,
Sarcophilus harrisii	ENSSHAG00000016094	2 retrocopies	retro_shar_123, retro_shar_626,
Ictidomys tridecemlineatus	ENSSTOG00000004024	3 retrocopies	retro_itri_1181, retro_itri_1774, retro_itri_359,
Tarsius syrichta	ENSTSYG00000005197	3 retrocopies	retro_tsyr_1835, retro_tsyr_359, retro_tsyr_714,
Tursiops truncatus	ENSTTRG00000003557	3 retrocopies	retro_ttru_1289, retro_ttru_1410, retro_ttru_516,