RetrogeneDB ID: retro_hsap_1008

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:58788382..58788920(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000258133
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSG00000143761
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:HGNC Symbol;Acc:652]

Sequence

>retro_hsap_1008
GGATTATCTTTTACCAACTTCTTTAAGGTCGTTTTTGGCAAAAAAGAAACGCTTGTCCTCATGGTGGGCCTAGATGCTGC
AGGCAAGATGATGATTCTGTATAAGCTGAAGCTGGTTGAGATTGTGACCACTGTTCCCATCACAGGCTTCAATGCAGATA
CATGGAGTCTAGGAACGTCAGCTTCACTGTGTGGGACATGGCAGGCCAGCACAAGATCTGGCCTCTGTGGTGCCACTACT
TCCAGAACACATAAGGCCTGATCTTTATGGAGGACAGTAGTGACAGAGAGCACATGAACAAGGCCCATGAGGAGCTCATG
AGGATGTTGGCTGAGGATGAGCTCTGGAATGCGGTCCCCCTGGTGTTCCCAACAAGTAGGCCCTTCTCAACACCATGAAC
ACCACTGAGATCACAGACAAGCTGGGGCTGCATTCCCTGCTCCACAGGAACTGATACATTCAGGCCACCTGTGGCACCTG
TGGTGACCAGCTCCATGAAGGACTGGACTGGCTGTCCAGTCAGCTCCAGAACTGGAAG

Alignment

ORF - retro_hsap_1008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.78 %
• Parental protein coverage: 99.45 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVET-VEYKNISFTVWDVGG
          G..F.N.FK..FGKKE...LMVGLDAAGK..ILYKLKL.EIVTT.P..GFN..T..E..N.SFTVWD..G
Retrocopy GLSFTNFFKVVFGKKETLVLMVGLDAAGKMMILYKLKLVEIVTTVPITGFNADT<MESRNVSFTVWDMAG

Parental  QDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVF-ANKQDLPNAMNAAEI
          Q.KI.PLW.HYFQNT.GLIF..DS.DRE..N.A.EELMRMLAEDEL..AV.LVF..NK..L.N.MN..EI
Retrocopy QHKIWPLWCHYFQNT*GLIFMEDSSDREHMNKAHEELMRMLAEDELWNAVPLVF<PNK*ALLNTMNTTEI

Parental  TDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK
          TDKLGLHSL.HRN.YIQATC.T.GD.L.EGLDWLS.QL.N.K
Retrocopy TDKLGLHSLLHRN*YIQATCGTCGDQLHEGLDWLSSQLQNWK

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	0.00 RPM	224.28 RPM
bodymap2_adrenal	0.00 RPM	197.98 RPM
bodymap2_brain	0.00 RPM	155.22 RPM
bodymap2_breast	0.00 RPM	148.99 RPM
bodymap2_colon	0.00 RPM	202.31 RPM
bodymap2_heart	0.11 RPM	152.25 RPM
bodymap2_kidney	0.00 RPM	223.68 RPM
bodymap2_liver	0.00 RPM	188.17 RPM
bodymap2_lung	0.00 RPM	436.08 RPM
bodymap2_lymph_node	0.00 RPM	226.92 RPM
bodymap2_ovary	0.00 RPM	175.38 RPM
bodymap2_prostate	0.00 RPM	278.44 RPM
bodymap2_skeletal_muscle	0.00 RPM	314.49 RPM
bodymap2_testis	0.04 RPM	234.06 RPM
bodymap2_thyroid	0.00 RPM	198.10 RPM
bodymap2_white_blood_cells	0.00 RPM	319.26 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1008 was not detected

EST

No EST(s) were mapped for retro_hsap_1008 retrocopy.

TSS

No TSS is located nearby retro_hsap_1008 retrocopy 5' end.

Lab

retro_hsap_1008 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1008 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Cavia porcellus	ENSCPOG00000021174	1 retrocopy	retro_cpor_1310,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Felis catus	ENSFCAG00000029374	1 retrocopy	retro_fcat_1829,
Homo sapiens	ENSG00000134108	1 retrocopy	retro_hsap_361,
Homo sapiens	ENSG00000134287	1 retrocopy	retro_hsap_36,
Homo sapiens	ENSG00000143761	3 retrocopies	retro_hsap_1008 , retro_hsap_1160, retro_hsap_3763,
Homo sapiens	ENSG00000168374	2 retrocopies	retro_hsap_1296, retro_hsap_4221,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Gorilla gorilla	ENSGGOG00000011263	5 retrocopies	retro_ggor_161, retro_ggor_2531, retro_ggor_3071, retro_ggor_801, retro_ggor_906,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Mus musculus	ENSMUSG00000048076	1 retrocopy	retro_mmus_1718,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Pan troglodytes	ENSPTRG00000002066	2 retrocopies	retro_ptro_112, retro_ptro_5,
Tupaia belangeri	ENSTBEG00000009218	9 retrocopies	retro_tbel_1943, retro_tbel_2224, retro_tbel_2310, retro_tbel_2358, retro_tbel_2662, retro_tbel_2770, retro_tbel_3103, retro_tbel_4217, retro_tbel_4624,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000014186	2 retrocopies	retro_ttru_1679, retro_ttru_347,