RetrogeneDB ID: retro_pabe_181

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:21123221..21123698(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000005607
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000017165
• Aliases: None
• Description: None

Sequence

>retro_pabe_181
ATGGAGAAGCTGCGGCGAGTCCTGAGCGGCCAGGACGACGAGGAGCAGGGCCTGACCGTGCAGGTCCTGGATGGCTCATC
CCTTAGTTTCAACACCAGATTGAAATGGTTTGCCATCTGCTTCGTATGTAGCATTTTCTTTTCTATTCTTGGAACTGGAT
TACTGTGGCTTCCGGGCGGCATAAAGCTTTCTGCAGTGTTTTATACCTTCGGCAATCTTGCTGCGTTAGCCAGTACATGC
TTTTTAATGGGACCAGTGAAGCAACTGAAGAAAATGTTTGAAACAACAAGATTGCTTGCAACAATTATTATGCTCTTGTG
TTTCATATTTACCCTGTGTGCTGCTCTTTGGTGGCATAAGAAGGGACTGGCTGTGTTATTCTGCATATTGCAGTTCTTGT
CAATGACCTGGTATAGCCTGTCGTACATCCCATATGCAAGGGATGCAGTTATTAAATGCTGTTCTTCTCTCCTAAGT

Alignment

ORF - retro_pabe_181 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.73 %
• Parental protein coverage: 90.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEKLRRVLSGQDDEEQGLTAQVLDASSLSFNTRLKWFAICFVCGIFFSILGTGLLWLPGGIKLFAVFYTL
          MEKLRRVLSGQDDEEQGLT.QVLD.SSLSFNTRLKWFAICFVC.IFFSILGTGLLWLPGGIKL.AVFYT.
Retrocopy MEKLRRVLSGQDDEEQGLTVQVLDGSSLSFNTRLKWFAICFVCSIFFSILGTGLLWLPGGIKLSAVFYTF

Parental  GNLAALASTCFLMGPVKQLKKMFETTRLLATIIMLLCFIFTLCAALW
          GNLAALASTCFLMGPVKQLKKMFETTRLLATIIMLLCFIFTLCAALW
Retrocopy GNLAALASTCFLMGPVKQLKKMFETTRLLATIIMLLCFIFTLCAALW

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	3.76 RPM	4.48 RPM
SRP007412_cerebellum	5.59 RPM	7.42 RPM
SRP007412_heart	1.51 RPM	1.96 RPM
SRP007412_kidney	4.61 RPM	5.90 RPM
SRP007412_liver	3.73 RPM	4.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_181 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_181 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_181 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009311	3 retrocopies	retro_amel_1244, retro_amel_1452, retro_amel_374,
Bos taurus	ENSBTAG00000002993	5 retrocopies	retro_btau_1458, retro_btau_1460, retro_btau_31, retro_btau_546, retro_btau_900,
Canis familiaris	ENSCAFG00000000811	2 retrocopies	retro_cfam_283, retro_cfam_551,
Equus caballus	ENSECAG00000019479	1 retrocopy	retro_ecab_1029,
Mus musculus	ENSMUSG00000073468	1 retrocopy	retro_mmus_164,
Oryctolagus cuniculus	ENSOCUG00000001200	1 retrocopy	retro_ocun_1492,
Otolemur garnettii	ENSOGAG00000006302	1 retrocopy	retro_ogar_1601,
Ochotona princeps	ENSOPRG00000003408	2 retrocopies	retro_opri_37, retro_opri_809,
Pongo abelii	ENSPPYG00000017165	1 retrocopy	retro_pabe_181 ,
Pteropus vampyrus	ENSPVAG00000012673	3 retrocopies	retro_pvam_1340, retro_pvam_465, retro_pvam_559,
Sus scrofa	ENSSSCG00000004020	1 retrocopy	retro_sscr_751,
Tupaia belangeri	ENSTBEG00000000045	2 retrocopies	retro_tbel_3277, retro_tbel_747,
Tursiops truncatus	ENSTTRG00000004447	2 retrocopies	retro_ttru_1353, retro_ttru_624,