RetrogeneDB ID: retro_hsap_4191

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:92064472..92065574(+)
• Located in intron of: ENSG00000187764

Retrocopy information

• Ensembl ID: ENSG00000231799
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PA2G4
• Ensembl ID: ENSG00000170515
• Aliases: PA2G4, EBP1, HG4-1, p38-2G4
• Description: proliferation-associated 2G4, 38kDa [Source:HGNC Symbol;Acc:8550]

Sequence

>retro_hsap_4191
ATGTCAGGCAAAGACGAGCAGCAGGAGCAAACTATCGCCGAGGACCTGGTCGTGACCAACTATAAGATGGGGGGGTGACA
TTGCCAATGGGGTACTTCGGTCCTTGGTGGACGCATCTAGCTCAGGTGTGTCAGTACTGAGCCTGTGTGAGAAAGGTGAT
GCCGTGATTATGCAAGAAACAGGGAAAATCTTCAAGAAAGAAAAAGAGATGAAGAAACGTATTGCTTTTCCCACCAGCAT
TTTGGTAAATAACTGTGTATGTCACTTCTCCCCTTTGAAGAGAGACCAGGATTATATTCTCAAGGAAGGTGACTTGGTAA
AAATTGACCTTGGGGTCCATGTGAATGGCTTCATCACTAATGTAGCTCGTACTTTTCTGACTGATGTAGCTCAGGGGACC
CAAGTAACAGGGAGGAAAGCAGATGTTATTAAGGCAGCTCACCGTTGTGCTGAAGCTGCCCCATGCCTGGTCACACCTGG
AAATCAGAACACACAAGTGACAGAAGCCTGGAACAAAGTTGCCCACTTATTTAACTGCATGCCAATAGAAGGTATGCTGT
CACACCAGCTGAAGCAGCATGTCATCGATGGAGAAAAAACCATTACCCAGATTCCCACAGACAAGCAGAAGAAGGACCAT
GAAAAAGCTGAATTTGAGGTACATGAAGTATATGCTGTGGATGTTCTCATCAGCTCAGGAAAGGGCAAGACCAAGGATGC
AGGAGAGAGAACCACTATGTACAAATGAGACCCCTCCAAACAGTATGGACTGAAAATGAAAACTTGACATGCCTTCTTCA
GTGACATGAAAAGGCGTTTTGATGCCATGCCATTTACTTCAAGAGCATGTGAAGATGAGAAGAAGGCTTGGATGGGTGTG
GTGGAGTGCGCCAAACATGAAATGCTGCAACCATTTAATGTTCTCTATGAGAAGGAGGGTGAATTTGTTGCCCAGTTTAA
ATTTACAGTTCTGCTCCTGCCCAATGGCCCCATGCAGATAACCAGTGGTCCCTTCCAGCCTGACCTCTATAAGTCTGAGA
TGAAGGTCCAGGATGCAGAGCTAAAGACCCTCCTCCAGAGTTCTGCAAGTCGAAAAACCCAG

Alignment

ORF - retro_hsap_4191 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.04 %
• Parental protein coverage: 93.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGEDEQQEQTIAEDLVVTKYKMGG-DIANRVLRSLVEASSSGVSVLSLCEKGDAMIMEETGKIFKKEKE
          MSG.DEQQEQTIAEDLVVT.YKMGG.DIAN.VLRSLV.ASSSGVSVLSLCEKGDA.IM.ETGKIFKKEKE
Retrocopy MSGKDEQQEQTIAEDLVVTNYKMGG>DIANGVLRSLVDASSSGVSVLSLCEKGDAVIMQETGKIFKKEKE

Parental  MKKGIAFPTSISVNNCVCHFSPLKSDQDYILKEGDLVKIDLGVHVDGFIANVAHTFVVDVAQGTQVTGRK
          MKK.IAFPTSI.VNNCVCHFSPLK.DQDYILKEGDLVKIDLGVHV.GFI.NVA.TF..DVAQGTQVTGRK
Retrocopy MKKRIAFPTSILVNNCVCHFSPLKRDQDYILKEGDLVKIDLGVHVNGFITNVARTFLTDVAQGTQVTGRK

Parental  ADVIKAAHLCAEAALRLVKPGNQNTQVTEAWNKVAHSFNCTPIEGMLSHQLKQHVIDGEKTIIQNPTDQQ
          ADVIKAAH.CAEAA..LV.PGNQNTQVTEAWNKVAH.FNC.PIEGMLSHQLKQHVIDGEKTI.Q.PTD.Q
Retrocopy ADVIKAAHRCAEAAPCLVTPGNQNTQVTEAWNKVAHLFNCMPIEGMLSHQLKQHVIDGEKTITQIPTDKQ

Parental  KKDHEKAEFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDPSKQYGLKMKTSRAFFSEVERRFDAMPFT
          KKDHEKAEFEVHEVYAVDVL.SSG.GK.KDAG.RTT.YK.DPSKQYGLKMKT..AFFS...RRFDAMPFT
Retrocopy KKDHEKAEFEVHEVYAVDVLISSGKGKTKDAGERTTMYK*DPSKQYGLKMKT*HAFFSDMKRRFDAMPFT

Parental  LRAFEDEKKARMGVVECAKHELLQPFNVLYEKEGEFVAQFKFTVLLMPNGPMRITSGPFEPDLYKSEMEV
          .RA.EDEKKA.MGVVECAKHE.LQPFNVLYEKEGEFVAQFKFTVLL.PNGPM.ITSGPF.PDLYKSEM.V
Retrocopy SRACEDEKKAWMGVVECAKHEMLQPFNVLYEKEGEFVAQFKFTVLLLPNGPMQITSGPFQPDLYKSEMKV

Parental  QDAELKALLQSSASRKTQ
          QDAELK.LLQSSASRKTQ
Retrocopy QDAELKTLLQSSASRKTQ

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
bodymap2_adipose	0.06 RPM	102.89 RPM
bodymap2_adrenal	0.68 RPM	101.45 RPM
bodymap2_brain	0.68 RPM	71.63 RPM
bodymap2_breast	0.10 RPM	69.57 RPM
bodymap2_colon	0.00 RPM	128.02 RPM
bodymap2_heart	0.06 RPM	41.59 RPM
bodymap2_kidney	0.21 RPM	64.89 RPM
bodymap2_liver	0.00 RPM	50.34 RPM
bodymap2_lung	0.00 RPM	93.58 RPM
bodymap2_lymph_node	0.13 RPM	72.80 RPM
bodymap2_ovary	0.04 RPM	115.14 RPM
bodymap2_prostate	0.00 RPM	106.95 RPM
bodymap2_skeletal_muscle	0.00 RPM	129.57 RPM
bodymap2_testis	0.02 RPM	110.08 RPM
bodymap2_thyroid	0.02 RPM	95.53 RPM
bodymap2_white_blood_cells	0.28 RPM	78.59 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4191 was not detected

EST

No EST(s) were mapped for retro_hsap_4191 retrocopy.

TSS

No TSS is located nearby retro_hsap_4191 retrocopy 5' end.

Lab

retro_hsap_4191 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4191 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007181	2 retrocopies	retro_chof_1089, retro_chof_1847,
Callithrix jacchus	ENSCJAG00000011811	2 retrocopies	retro_cjac_4214, retro_cjac_4215,
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,
Mus musculus	ENSMUSG00000025364	1 retrocopy	retro_mmus_2803,
Nomascus leucogenys	ENSNLEG00000017544	6 retrocopies	retro_nleu_1212, retro_nleu_1260, retro_nleu_163, retro_nleu_3024, retro_nleu_506, retro_nleu_612,
Oryctolagus cuniculus	ENSOCUG00000017342	1 retrocopy	retro_ocun_1733,
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,
Pan troglodytes	ENSPTRG00000005076	6 retrocopies	retro_ptro_1289, retro_ptro_1389, retro_ptro_1940, retro_ptro_2471, retro_ptro_2846, retro_ptro_3263,
Sus scrofa	ENSSSCG00000000377	1 retrocopy	retro_sscr_338,
Sus scrofa	ENSSSCG00000022666	2 retrocopies	retro_sscr_1143, retro_sscr_337,
Tarsius syrichta	ENSTSYG00000006777	1 retrocopy	retro_tsyr_746,
Vicugna pacos	ENSVPAG00000009523	1 retrocopy	retro_vpac_2,