RetrogeneDB ID: retro_pabe_1518

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:62964003..62964441(-)
• Located in intron of: ENSPPYG00000008584

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG12
• Ensembl ID: ENSPPYG00000015699
• Aliases: None
• Description: ubiquitin-like protein ATG12 [Source:RefSeq peptide;Acc:NP_001126258]

Sequence

>retro_pabe_1518
AGAGTCTCTCCAAGCAAGATGGTGGAGGAGCCGCAGTCCATATTGCAGCTTCCTCCCTCAAGTGCTGCTGGAAGGGAAGG
ACTTACGGAGGTCTCCCCAGAAACAACCATCCCAGAGCCCCCATCTTCCGCTGCAGGTTCCCCAGGAACAGAGGAACCTG
CTGGTGACACCAAGAAAAAAATTGACATTTTGCTAAAGGCTGTGGGAGATACTCCTATTATGAAAACAAAGAAGTGGGCA
GTAGAGCGAACATGAACCATCCAAGGACTCATTGACTTTAGCAAAAAGTTTCTTAAACTTGTGGCCTCAGAACAGTTGTT
TATTTATGTGAATCAGTCCTTTGCTCCTTCCCCAGACCAGGAAGTTGGAACTCTCTATGAGTGTTTTGGCAGTGATGGTA
AACTGGTTTTACATTACTGCAAGTCTCAGGCATGGGGA

Alignment

ORF - retro_pabe_1518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.84 %
• Parental protein coverage: 78.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVSPSKMAEEPQTVLQLPPSSAAGGEGLTDVSPETTTPEPPSSAAVSPGTEEPAGDTKKKIDILLKAVGD
          RVSPSKM.EEPQ..LQLPPSSAAG.EGLT.VSPETT.PEPPSSAA.SPGTEEPAGDTKKKIDILLKAVGD
Retrocopy RVSPSKMVEEPQSILQLPPSSAAGREGLTEVSPETTIPEPPSSAAGSPGTEEPAGDTKKKIDILLKAVGD

Parental  TPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKLVLHYC
          TPIMKTKKWAVERT.TIQGLIDF.KKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKLVLHYC
Retrocopy TPIMKTKKWAVERT*TIQGLIDFSKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKLVLHYC

Parental  KSQAWG
          KSQAWG
Retrocopy KSQAWG

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	31.46 RPM
SRP007412_cerebellum	0.00 RPM	34.90 RPM
SRP007412_heart	0.00 RPM	18.00 RPM
SRP007412_kidney	0.00 RPM	16.97 RPM
SRP007412_liver	0.00 RPM	15.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1518 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1518 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1518 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1860
Pan troglodytes	retro_ptro_1240
Gorilla gorilla	retro_ggor_2150

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004464	1 retrocopy	retro_chof_1745,
Cavia porcellus	ENSCPOG00000007187	2 retrocopies	retro_cpor_865, retro_cpor_944,
Equus caballus	ENSECAG00000012452	1 retrocopy	retro_ecab_883,
Echinops telfairi	ENSETEG00000018837	1 retrocopy	retro_etel_1721,
Homo sapiens	ENSG00000145782	1 retrocopy	retro_hsap_1860,
Gorilla gorilla	ENSGGOG00000016888	2 retrocopies	retro_ggor_1814, retro_ggor_2150,
Loxodonta africana	ENSLAFG00000015307	1 retrocopy	retro_lafr_450,
Myotis lucifugus	ENSMLUG00000002759	1 retrocopy	retro_mluc_2259,
Pongo abelii	ENSPPYG00000015699	3 retrocopies	retro_pabe_1518 , retro_pabe_1519, retro_pabe_2158,
Pan troglodytes	ENSPTRG00000017154	2 retrocopies	retro_ptro_1240, retro_ptro_1748,
Rattus norvegicus	ENSRNOG00000000157	1 retrocopy	retro_rnor_2811,
Ictidomys tridecemlineatus	ENSSTOG00000011755	1 retrocopy	retro_itri_156,