RetrogeneDB ID: retro_pabe_2158

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:114948485..114948948(-)
• Located in intron of: ENSPPYG00000013223

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_2158
CCCTTACCACCCCTGAACAATCCTTTTCAAAATCTCAGCTGGGACCTAACAAGATGGCAGAAGCTGAAGACCATGTCACA
GCTACCTCCCTTAACTGCTGCTGGCAGCAAAGGACTTACTCTAGAGGTCTCCCCAAAACAGGCACTTCAGACCCCCCTTA
TTCCACTGTAGTTTCCCTGGGACACAGGATCCTGCTGGCAACATCAAGAAAAATCTGACATCCTACTAAAGGCTGTGGGA
CATGTTCCTATTATGAATACAAAGAAGCAGGCAGTACAGTGAACTCAAACCATTCAAAGACTCCTTGACTTCATCAAAAA
AGTTCCTTAAACTTGCAACCTCAGTTGTTTATTTATGTGAGTCAGGCTTTGCTTTTTCCCTGGACCAGGAATTTGGAACC
TTCTATGAGTGTTTCAGCAGTGATGGTAAACTAGTTCTACATTACTGCAAATCTCAGGCATGG

Alignment

ORF - retro_pabe_2158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.02 %
• Parental protein coverage: 83.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PLHALSRYFRSRVSPSKMAEEPQTVLQLPPSSAAGGEGLT-DVS-PETTTPEPPSSAAVS-PGTEEPAGD
          PL..L...F..............T..QLPP..AAG..GLT..VS.P.T.T..PP.S..VS.PGT..PAG.
Retrocopy PLPPLNNPFQNLSWDLTRWQKLKTMSQLPPLTAAGSKGLTLEVS<PKTGTSDPPYSTVVS<PGTQDPAGN

Parental  TKK-KIDILLKAVGDTPIMKTKKWAVERTRTIQGLIDFI-KKFLKLVASEQLFIYVNQS-FAPSPDQEVG
          .KK.K.DILLKAVG..PIM.TKK.AV..T.TIQ.L.DFI.KKFLKL..S.....Y...S.FA.S.DQE.G
Retrocopy IKK<KSDILLKAVGHVPIMNTKKQAVQ*TQTIQRLLDFI>KKFLKLATS---VVYLCESGFAFSLDQEFG

Parental  TLYECFGSDGKLVLHYCKSQAW
          T.YECF.SDGKLVLHYCKSQAW
Retrocopy TFYECFSSDGKLVLHYCKSQAW

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	0.11 RPM	31.46 RPM
SRP007412_cerebellum	0.00 RPM	34.90 RPM
SRP007412_heart	0.06 RPM	18.00 RPM
SRP007412_kidney	0.03 RPM	16.97 RPM
SRP007412_liver	0.31 RPM	15.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2158 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2158 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2158 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1748
Gorilla gorilla	retro_ggor_1814

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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,