RetrogeneDB ID: retro_pabe_2345

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:130205270..130205533(-)
• Located in intron of: ENSPPYG00000014078

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000029910
• Aliases: None
• Description: None

Sequence

>retro_pabe_2345
ATGGCCAAGAACAAACTGAAGAGGGAAGAAGTCCAGCAATGTATTTCACATATCCAGTTAAAAAAACTTTAGGGTTCAAA
ACAAAGCAAAACCAATTACCACTAATCTTGTAAACAATTTAAACACTGGAAAAGTTAGCAGAGTGAATAAAGTTTTTATA
CATATACAGAAAACAACTTGCTCACTTCTCAAAAGGCATTCCCCTTGAACCTCTGCAGAAACGGCTGATTCCTCAGCAGC
ATCATGACAACAAACCAGTTAAT

Alignment

ORF - retro_pabe_2345 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.03 %
• Parental protein coverage: 89. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKNKL-RGPKSRNVFHIASQKNFKAKNKAKPVTTNLKKINIMNEEKVNRVNKAFVNVQK-ELAHFSKST
          MAKNKL.RG.KS.NVFHI.S.KNF...NKAKP.TTNL...N..N..KV.RVNK.F...QK..LAHFSK..
Retrocopy MAKNKL>RGKKSSNVFHISS*KNFRVQNKAKPITTNL--VNNLNTGKVSRVNKVFIHIQK>QLAHFSKGI

Parental  SLEPLQKELIPQQRHESKPVN
          .LEPLQK.LIPQQ.H..KPVN
Retrocopy PLEPLQKRLIPQQHHDNKPVN

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	1.33 RPM
SRP007412_cerebellum	0.00 RPM	3.77 RPM
SRP007412_heart	0.00 RPM	5.24 RPM
SRP007412_kidney	0.00 RPM	7.96 RPM
SRP007412_liver	0.03 RPM	7.80 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2345 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2345 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2345 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2609
Pan troglodytes	retro_ptro_1759
Gorilla gorilla	retro_ggor_1828
Macaca mulatta	retro_mmul_1475
Callithrix jacchus	retro_cjac_1556

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002409	2 retrocopies	retro_amel_1005, retro_amel_1049,
Bos taurus	ENSBTAG00000032227	2 retrocopies	retro_btau_158, retro_btau_7,
Callithrix jacchus	ENSCJAG00000000379	5 retrocopies	retro_cjac_1214, retro_cjac_1556, retro_cjac_1984, retro_cjac_2448, retro_cjac_2762,
Cavia porcellus	ENSCPOG00000021965	5 retrocopies	retro_cpor_201, retro_cpor_554, retro_cpor_765, retro_cpor_841, retro_cpor_962,
Felis catus	ENSFCAG00000026366	1 retrocopy	retro_fcat_450,
Homo sapiens	ENSG00000176731	4 retrocopies	retro_hsap_2609, retro_hsap_3163, retro_hsap_3606, retro_hsap_52,
Gorilla gorilla	ENSGGOG00000027464	4 retrocopies	retro_ggor_1218, retro_ggor_1353, retro_ggor_1828, retro_ggor_2433,
Loxodonta africana	ENSLAFG00000032612	4 retrocopies	retro_lafr_1083, retro_lafr_1242, retro_lafr_911, retro_lafr_944,
Myotis lucifugus	ENSMLUG00000006155	1 retrocopy	retro_mluc_1272,
Macaca mulatta	ENSMMUG00000006381	3 retrocopies	retro_mmul_1475, retro_mmul_2490, retro_mmul_537,
Mus musculus	ENSMUSG00000078784	3 retrocopies	retro_mmus_257, retro_mmus_2950, retro_mmus_3313,
Pongo abelii	ENSPPYG00000029910	3 retrocopies	retro_pabe_2345 , retro_pabe_2630, retro_pabe_3633,
Pan troglodytes	ENSPTRG00000020385	5 retrocopies	retro_ptro_1759, retro_ptro_2275, retro_ptro_2437, retro_ptro_2982, retro_ptro_471,
Rattus norvegicus	ENSRNOG00000038902	2 retrocopies	retro_rnor_2600, retro_rnor_496,
Sus scrofa	ENSSSCG00000006144	2 retrocopies	retro_sscr_342, retro_sscr_96,