RetrogeneDB ID: retro_pabe_2993

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:114856799..114857981(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PA2G4
• Ensembl ID: ENSPPYG00000025851
• Aliases: None
• Description: proliferation-associated protein 2G4 [Source:RefSeq peptide;Acc:NP_001124717]

Sequence

>retro_pabe_2993
ATGTAGGGTGAGGACGAGCAGCAGAAGCAAACTATCGCTGAAGACCTGGTTGTGACCAAGTATAAGATGGGGGGCGACAT
TGCCAACCAGGTACTTAGGTCCTTGGTGGAAGCATCTAGCTCAGGTGTATTGGTACTGAGCCTGTGTGAGAAAAGTGATG
CCATGATTATGGAAGAAACAGGGAAAATCTTCAAGAAAGAAAAGGAAATGAAGAAAGGCATTGCTTTTCCCACCAGTATT
TCAGTAAATAACTGTGTATGTCACTTCTCCCCTTTGAAGAGTGGCCAGGATTATATTCTCAAGGAAGGTGACATGGTAAA
AATTGACCTTGGGGTCCTTGTGCATGGCTTCTTGGCTAATGTAGCTCATACTTTTGTGGTTGATGTAGCTCAGGGGACCC
AAGTAACAGGGAGGAAAGCAGATGTTATTAAGGCAGCTCACCTTTGTGCTGAAGCTGCCCTACGCCTGGTCAAACCTGGA
AATCAGAACACACAAGTGACAGAAGCCTGGAACAAATTTGGCCAGTAATTTAACTACACGCCAATAGAAGGTATGCTGTC
ACACCAGTTGAAGCAGCATGTCATCGATGGAGAAAAAACCATTATCCAGAATCCCACAGACCAGCAGAAGAAGGACCACG
AAAAAGCTGAATTTGAGGTATATGAAGTATATGCTGTGGATGTTCTCATCAGCTCAGGAGAGGGCAAGGCCAAGGATGCA
GGACAGAGAACCACTATTTACAAATGAGACCCCCCTAAAGCGCATGGACTGAAAATGAAAACTTCACATGCCTTCTTCAG
TGGATGGAAAGGCGTTTTGATGCCATGCTGTTTACTTTAAGAGCATTTGAAGATGAGAAGAAGGCTCGGATAGGTGTGGT
GGAGTGCGCCAAACATGAACTGCTGCAACCATTTAATGTTCTCCATGAGAAGGAGGGTGAATTTTTTGCCCAGTTTGAAT
TTACAGTTCTGCTTATGCCCAATGGCCCCATGCGGATAACCAGTAGTCCCCTCAAGCCTGATCTCTACAAGTCTGAGATG
GAGGTCCAGGATGCAGAGCTAAAGGCCCTCCTCGAGTTCTGCAAGTCGAAAAACCCAGCAAAAAAAAAAAAAAAAGAAGG
CCTCCAAGACTGCAGAAAATGCCACCAGTGGGGAAATATTAGAAGAAAATGAAGCTGGGGAC

Alignment

ORF - retro_pabe_2993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSGEDEQQEQTIAEDLVVTKYKMGGDIANRVLRSLVEASSSGVSVLSLCEKGDAMIMEETGKIFKKEKEM
          M.GEDEQQ.QTIAEDLVVTKYKMGGDIAN.VLRSLVEASSSGV.VLSLCEK.DAMIMEETGKIFKKEKEM
Retrocopy M*GEDEQQKQTIAEDLVVTKYKMGGDIANQVLRSLVEASSSGVLVLSLCEKSDAMIMEETGKIFKKEKEM

Parental  KKGIAFPTSISVNNCVCHFSPLKSDQDYILKEGDLVKIDLGVHVDGFIANVAHTFVVDVAQGTQVTGRKA
          KKGIAFPTSISVNNCVCHFSPLKS.QDYILKEGD.VKIDLGV.V.GF.ANVAHTFVVDVAQGTQVTGRKA
Retrocopy KKGIAFPTSISVNNCVCHFSPLKSGQDYILKEGDMVKIDLGVLVHGFLANVAHTFVVDVAQGTQVTGRKA

Parental  DVIKAAHLCAEAALRLVKPGNQNTQVTEAWNKVAHSFNCTPIEGMLSHQLKQHVIDGEKTIIQNPTDQQK
          DVIKAAHLCAEAALRLVKPGNQNTQVTEAWNK....FN.TPIEGMLSHQLKQHVIDGEKTIIQNPTDQQK
Retrocopy DVIKAAHLCAEAALRLVKPGNQNTQVTEAWNKFGQ*FNYTPIEGMLSHQLKQHVIDGEKTIIQNPTDQQK

Parental  KDHEKAEFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDPSKQYGLKMKTSRAFFSE-VERRFDAMPFT
          KDHEKAEFEV.EVYAVDVL.SSGEGKAKDAGQRTTIYK.DP.K..GLKMKTS.AFFS...ERRFDAM.FT
Retrocopy KDHEKAEFEVYEVYAVDVLISSGEGKAKDAGQRTTIYK*DPPKAHGLKMKTSHAFFSG<MERRFDAMLFT

Parental  LRAFEDEKKARMGVVECAKHELLQPFNVLYEKEGEFVAQFKFTVLLMPNGPMRITSGPFEPDLYKSEMEV
          LRAFEDEKKAR.GVVECAKHELLQPFNVL.EKEGEF.AQF.FTVLLMPNGPMRITS.P..PDLYKSEMEV
Retrocopy LRAFEDEKKARIGVVECAKHELLQPFNVLHEKEGEFFAQFEFTVLLMPNGPMRITSSPLKPDLYKSEMEV

Parental  QDAELKALLQ-SSASRKTQKKKKKKASKTAENATSGETLEENEAGD
          QDAELKALL..S............KASKTAENATSGE.LEENEAGD
Retrocopy QDAELKALLE>SASRKTQXXXXXXKASKTAENATSGEILEENEAGD

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	51.81 RPM
SRP007412_cerebellum	0.00 RPM	46.69 RPM
SRP007412_heart	0.06 RPM	25.62 RPM
SRP007412_kidney	0.00 RPM	40.41 RPM
SRP007412_liver	0.03 RPM	34.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2993 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2993 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2993 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3646

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007181	2 retrocopies	retro_chof_1089, retro_chof_1847,
Homo sapiens	ENSG00000170515	6 retrocopies	retro_hsap_1930, retro_hsap_2413, retro_hsap_2868, retro_hsap_3646, retro_hsap_4191, retro_hsap_4895,
Macaca mulatta	ENSMMUG00000002164	2 retrocopies	retro_mmul_1168, retro_mmul_2631,
Nomascus leucogenys	ENSNLEG00000017544	6 retrocopies	retro_nleu_1212, retro_nleu_1260, retro_nleu_163, retro_nleu_3024, retro_nleu_506, retro_nleu_612,
Pongo abelii	ENSPPYG00000025851	7 retrocopies	retro_pabe_1595, retro_pabe_1778, retro_pabe_2375, retro_pabe_2869, retro_pabe_2993 , retro_pabe_3430, retro_pabe_3807,
Sus scrofa	ENSSSCG00000000377	1 retrocopy	retro_sscr_338,
Sus scrofa	ENSSSCG00000022666	2 retrocopies	retro_sscr_1143, retro_sscr_337,
Vicugna pacos	ENSVPAG00000009523	1 retrocopy	retro_vpac_2,