RetrogeneDB ID: retro_hsap_1609

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:85724452..85725314(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000259449
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MKI67IP
• Ensembl ID: ENSG00000155438
• Aliases: NIFK, MKI67IP, Nopp34
• Description: MKI67 (FHA domain) interacting nucleolar phosphoprotein [Source:HGNC Symbol;Acc:17838]

Sequence

>retro_hsap_1609
ATGGTGGCCTTTTCCAACCTGGCTGGGCCAATCCAGTCACTGAACCTGAAGGAAGATGCCAAGTTTCAGAAGAAAGTGGC
ACAGGTTCGCAAGCACATAACCCAGTGAAAAAAACAAGAACAGCTTACTCCTGGAGTAGTCTATGTGTGCCACCTACCTA
ACCTACTGAACAAAACCCAGATCCTTTCCTATTTCTCCCAGTGTGGCACTGTTACAAGGTTCAGACTATCCAGAAAGAAA
AGGACTGGAAATAGCAAAGGCTATGCATGTGTGGAGTGTGAGTCTGAGGATATTGCCAAGATAGTTGCTGAAACGATGAA
CAACTACCTGTTTGGTGAAAGACTCTCAGAGTGTCATTTTATGCCACCTGAAAAATTCAAAAAGAACTCTTTAAAGACTG
GGATATTCCATTTAAGCAGCCATCATATCTGTCAGTGAAACAGCATAATCAGAATCGGCACTTACACAAAAGCTGCGAAT
AGAGGGACGATTTAAAAAGAAAGAAAGATTACTCAGGAAGAAATTAGCTTATAAAGGAATTGATTATGATTTTCCTTCTT
TGATTTTACAGAAAATGGAAAGTATTTCAAAAACGAATCATCTGATGTCTACAAAAGGCCACGTTTTACGTAAGAAGAAG
AAAAAGGTTTTAGGCATTCCTGACACTCCTGAGAAGACTGTGGATACCCAGGGCCCCACACCGGTTTGTACATCAACATT
TTTGGAGAGACAAAAATCTGAAGTGGCTGAAATGAATGATGATGATGAAGATAATGAAATAGTTTTTGAAAAGCCCATAT
CCTGTGTAAAAGAAGAAATACAAGAGACTCAAACACCTACACATTCACAGAAAAAAAGACAA

Alignment

ORF - retro_hsap_1609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.38 %
• Parental protein coverage: 98.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATFSGPAGPILSLNPQEDVEFQKEVAQVRKRITQRKKQEQLTPGVVYVRHLPNLLDETQIFSYFSQFGT
          M..FS..AGPI.SLN..ED..FQK.VAQVRK.ITQ.KKQEQLTPGVVYV.HLPNLL..TQI.SYFSQ.GT
Retrocopy MVAFSNLAGPIQSLNLKEDAKFQKKVAQVRKHITQ*KKQEQLTPGVVYVCHLPNLLNKTQILSYFSQCGT

Parental  VTRFRLSRSKRTGNSKGYAFVEFESEDVAKIVAETMNNYLFGERLLECHFMPPEK-VHKELFKDWNIPFK
          VTRFRLSR.KRTGNSKGYA.VE.ESED.AKIVAETMNNYLFGERL.ECHFMPPEK...KELFKDW.IPFK
Retrocopy VTRFRLSRKKRTGNSKGYACVECESEDIAKIVAETMNNYLFGERLSECHFMPPEK<IQKELFKDWDIPFK

Parental  QPSYPSVKRYNRNR-TLTQKLRMEERFKKKERLLRKKLAKKGIDYDFPSLILQKTESISKTNRQTSTKGQ
          QPSY.SVK..N.NR..LTQKLR.E.RFKKKERLLRKKLA.KGIDYDFPSLILQK.ESISKTN...STKG.
Retrocopy QPSYLSVKQHNQNR<ALTQKLRIEGRFKKKERLLRKKLAYKGIDYDFPSLILQKMESISKTNHLMSTKGH

Parental  VLRKKKKKVSGTLDTPEKTVDSQGPTPVCTPTFLERRKSQVAELNDDDKDDEIVFKQPISCVKEEIQETQ
          VLRKKKKKV.G..DTPEKTVD.QGPTPVCT.TFLER.KS.VAE.NDDD.D.EIVF..PISCVKEEIQETQ
Retrocopy VLRKKKKKVLGIPDTPEKTVDTQGPTPVCTSTFLERQKSEVAEMNDDDEDNEIVFEKPISCVKEEIQETQ

Parental  TPTHSRKKRR
          TPTHS.KKR.
Retrocopy TPTHSQKKRQ

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	18.01 RPM
bodymap2_adrenal	0.00 RPM	37.81 RPM
bodymap2_brain	0.02 RPM	19.13 RPM
bodymap2_breast	0.00 RPM	15.43 RPM
bodymap2_colon	0.00 RPM	29.53 RPM
bodymap2_heart	0.00 RPM	9.93 RPM
bodymap2_kidney	0.00 RPM	30.30 RPM
bodymap2_liver	0.00 RPM	21.04 RPM
bodymap2_lung	0.00 RPM	19.08 RPM
bodymap2_lymph_node	0.00 RPM	24.80 RPM
bodymap2_ovary	0.00 RPM	47.96 RPM
bodymap2_prostate	0.00 RPM	31.90 RPM
bodymap2_skeletal_muscle	0.00 RPM	31.32 RPM
bodymap2_testis	0.00 RPM	34.84 RPM
bodymap2_thyroid	0.00 RPM	39.43 RPM
bodymap2_white_blood_cells	0.00 RPM	40.95 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1609 was not detected

EST

No EST(s) were mapped for retro_hsap_1609 retrocopy.

TSS

No TSS is located nearby retro_hsap_1609 retrocopy 5' end.

Lab

retro_hsap_1609 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1609 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019387	1 retrocopy	retro_btau_1516,
Choloepus hoffmanni	ENSCHOG00000002227	5 retrocopies	retro_chof_1061, retro_chof_1449, retro_chof_1735, retro_chof_236, retro_chof_2480,
Callithrix jacchus	ENSCJAG00000013386	1 retrocopy	retro_cjac_3076,
Dasypus novemcinctus	ENSDNOG00000005017	2 retrocopies	retro_dnov_1869, retro_dnov_2487,
Erinaceus europaeus	ENSEEUG00000008535	3 retrocopies	retro_eeur_530, retro_eeur_550, retro_eeur_91,
Homo sapiens	ENSG00000155438	5 retrocopies	retro_hsap_1077, retro_hsap_1596, retro_hsap_1609 , retro_hsap_1611, retro_hsap_553,
Gorilla gorilla	ENSGGOG00000023498	4 retrocopies	retro_ggor_1213, retro_ggor_1923, retro_ggor_2225, retro_ggor_850,
Loxodonta africana	ENSLAFG00000030731	1 retrocopy	retro_lafr_500,
Microcebus murinus	ENSMICG00000015787	1 retrocopy	retro_mmur_990,
Myotis lucifugus	ENSMLUG00000006481	2 retrocopies	retro_mluc_1217, retro_mluc_1369,
Macaca mulatta	ENSMMUG00000020928	11 retrocopies	retro_mmul_1444, retro_mmul_1544, retro_mmul_2149, retro_mmul_2151, retro_mmul_2225, retro_mmul_2226, retro_mmul_2389, retro_mmul_690, retro_mmul_696, retro_mmul_697, retro_mmul_752,
Monodelphis domestica	ENSMODG00000000152	2 retrocopies	retro_mdom_1271, retro_mdom_737,
Nomascus leucogenys	ENSNLEG00000001163	4 retrocopies	retro_nleu_1756, retro_nleu_1942, retro_nleu_2022, retro_nleu_669,
Pongo abelii	ENSPPYG00000025875	2 retrocopies	retro_pabe_2248, retro_pabe_510,
Pan troglodytes	ENSPTRG00000012419	5 retrocopies	retro_ptro_1072, retro_ptro_1077, retro_ptro_1080, retro_ptro_1378, retro_ptro_415,
Pteropus vampyrus	ENSPVAG00000016707	1 retrocopy	retro_pvam_134,
Sorex araneus	ENSSARG00000006252	1 retrocopy	retro_sara_362,
Tupaia belangeri	ENSTBEG00000001123	4 retrocopies	retro_tbel_1731, retro_tbel_3479, retro_tbel_4589, retro_tbel_926,
Vicugna pacos	ENSVPAG00000005847	2 retrocopies	retro_vpac_136, retro_vpac_265,