RetrogeneDB ID: retro_pabe_1669

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:23896727..23897330(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000003894
• Aliases: None
• Description: None

Sequence

>retro_pabe_1669
GCAGCGGAAGCAGATTGAACTCTCTTTGTGGGCAACCTTGAAACGAAAGTGACCGAGGAGCTCTTTTTCGAGCTTTTCCA
CCAGGCTGGGCCAGTAATAAAGGTGAAAATTCCAAAAGATAAGGATGGTAAACCAAAGCAGTTTGCGTTTGTGAATTTCA
AACATGAAGTATCTGTTCCTTATGCAATGAATCTACTTAATGGAATCAAACTTTATGGAAGGCCTATCAAAATTCCATTT
AGATCAGGAAGTAGTCATGCCTCACAAGATGTCAGTTTGTCATATCCCCAGCATCATGTTGGAAATTCAAGCCCTACCTC
TACATTTCCTAGCAGCAGGTATGAAAGGACTATGGATAACATGACTTCATCAGCACAGATAATTCAGAGATCTTTCTCTT
CTCCAGAAAATTTTCAGAGACAAGCAGTGATGAACAGTGCTTTGAGACAAATGTCATATGGTGGAAAATTTGGTTCTTCA
CCTCTGGATCAATTAGGATTTTCACCATCAGTTCAATCACACAGTCATAGTTTTAACCAGTCTTCAAGCTCCCAGTGGCA
CCAAGGTACACCATCATCACAGCGTAAAGTCAGAATGAATTCT

Alignment

ORF - retro_pabe_1669 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.52 %
• Parental protein coverage: 75.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAEADRTLFVGNLETKVTEELLFELFHQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIK
          AAEAD.TLFVGNLETKVTEEL.FELFHQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIK
Retrocopy AAEAD*TLFVGNLETKVTEELFFELFHQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIK

Parental  LYGRPIKIQFRSGSSHASQDVSLSYPQHHVGNSSPTSTSPSSRYERTMDNMTSSAPIIQRSFSSPENFQR
          LYGRPIKI.FRSGSSHASQDVSLSYPQHHVGNSSPTST.PSSRYERTMDNMTSSA.IIQRSFSSPENFQR
Retrocopy LYGRPIKIPFRSGSSHASQDVSLSYPQHHVGNSSPTSTFPSSRYERTMDNMTSSAQIIQRSFSSPENFQR

Parental  QAVMNSALRQMSYSGKFGSSPLDQSGFSPSVQSHSHSFNQSSSSQWRHGTPSSQRKVRMNS
          QAVMNSALRQMSY.GKFGSSPLDQ.GFSPSVQSHSHSFNQSSSSQW..GTPSSQRKVRMNS
Retrocopy QAVMNSALRQMSYGGKFGSSPLDQLGFSPSVQSHSHSFNQSSSSQWHQGTPSSQRKVRMNS

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	3.48 RPM
SRP007412_cerebellum	0.12 RPM	9.12 RPM
SRP007412_heart	0.00 RPM	4.73 RPM
SRP007412_kidney	0.10 RPM	8.72 RPM
SRP007412_liver	0.06 RPM	7.77 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1669 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1669 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1669 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013514	1 retrocopy	retro_cfam_1021,
Choloepus hoffmanni	ENSCHOG00000012747	1 retrocopy	retro_chof_570,
Homo sapiens	ENSG00000076053	1 retrocopy	retro_hsap_2283,
Gorilla gorilla	ENSGGOG00000009941	1 retrocopy	retro_ggor_1696,
Loxodonta africana	ENSLAFG00000012444	1 retrocopy	retro_lafr_892,
Myotis lucifugus	ENSMLUG00000023234	2 retrocopies	retro_mluc_1555, retro_mluc_587,
Monodelphis domestica	ENSMODG00000013918	1 retrocopy	retro_mdom_535,
Mus musculus	ENSMUSG00000042396	1 retrocopy	retro_mmus_2436,
Nomascus leucogenys	ENSNLEG00000007323	1 retrocopy	retro_nleu_409,
Oryctolagus cuniculus	ENSOCUG00000003342	1 retrocopy	retro_ocun_924,
Otolemur garnettii	ENSOGAG00000016857	1 retrocopy	retro_ogar_3103,
Pongo abelii	ENSPPYG00000000912	1 retrocopy	retro_pabe_1124,
Pongo abelii	ENSPPYG00000003894	1 retrocopy	retro_pabe_1669 ,
Pan troglodytes	ENSPTRG00000004305	1 retrocopy	retro_ptro_1617,
Ictidomys tridecemlineatus	ENSSTOG00000012459	1 retrocopy	retro_itri_889,
Tursiops truncatus	ENSTTRG00000001515	3 retrocopies	retro_ttru_1316, retro_ttru_1441, retro_ttru_478,
Vicugna pacos	ENSVPAG00000006300	1 retrocopy	retro_vpac_311,