RetrogeneDB ID: retro_hsap_4173

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:46912526..46913970(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000234217
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBPJ
• Ensembl ID: ENSG00000168214
• Aliases: RBPJ, AOS3, CBF1, IGKJRB, IGKJRB1, KBF2, RBP-J, RBPJK, RBPSUH, SUH, csl
• Description: recombination signal binding protein for immunoglobulin kappa J region [Source:HGNC Symbol;Acc:5724]

Sequence

>retro_hsap_4173
ATGGCATGGATTAAAAGGAAATTTGGTAAGTGGCCTCCATTTAAACGACTTACTAGGGAAGCTATGTGAAATTATTTAAA
AGGGTAAGGGGATCAAATAGTACTTAGCCTTCATGCAAAAGTTGTACAGAAGTCATATGGAAATGAAAAAAGGTTTTTTT
TGCCCTCCCCCTTGTGTATATCTTATGGGCAGTGGATGGAAGAAAATAAAATAACAAATGAAATGCGATGGTTGTTCTGA
ACAAGGGTCTCAACCAAGTGCATTTATTGGCATAGGAAATAGTGACCAAGAAATGCAGCAGCTAAACTTGGAAGGAAAGA
ACTATTGCACAGCCAAAACATTGTACATATCTGATTTAGACAAGCAAAAGCACTTCATGTTGTCTGTAAAGGTGTTCTAT
GGCAACAGTGATGACATTGGTGTGTTCCTCAGCAAGTCGTCCAAACCTTCCAAAAAGAAGCAGTCATTGAAAAATGCTGA
CTTATGCATTGCCTCAGGAAAAAAGGTGGCTCTGTTTAATCGACTACTATCCCAGACAGTTAGTACCAGATACTTGCACG
TAGAAAGAGGTAATTTTCATGCTAGTTCACAGCAATGGGGAGCATTTTACATTATTCTTGGATGATGATGGATCAGAAGG
AGAAGAATTCACAGTCTGAGATGGCTACATTCATTATGGACAAACAGTCAAACTTGTGTGCTCAGTTACTGGCATGGCAC
TCCCAAGATTGATAATTAGGAAAGTTGATAAGCAGACCACATTATTGGATGCAGATGATCCTGTGTCACAACTCCATAAA
TGTGCATTTGACCTTGAGGATACAGAAAGAAAGTACTTATGCCTTTCTCAAGAAAGAATAATTCAATTTCAGGCCACTCC
ATGCCCAAAAGAACCAAATAAAGAGAAGATAAATGATGGTGCTTCCTGGGCAATCATTAGCACACATAAGGCGAAGCATA
CATTTTATGAGAGAGTGGGCCCTGTCCTTGCCCTGGTCATGCCTCCGCCTGTCGTAGAGAGCCTTAAGTTGAATGGCGGT
GGGGACGAACCAATGCTTGAACTTACAGGACAGAATTTCACTCCAAATTTACAAGTGTGGTTTGGGGATGTAGAAGCTGA
AGCTATGTACAGGTGTGGAGAGAGTATGCTCGTGTTGTCCCAGACGTTTCTGCATTCTGAGAAGGTTGGAGATAGGTCCA
GCAACCAATACAGGTTTCAGTAACTTTGGTCCGAAATGATGGAATCATATATTCCACCAGCCTTACCTTTACCTACACAC
CAGAAGCAGGGCCGCGGCCACATTGCAGTGTAGCAGGTGCCATCCTTCAAGCCAGTTCAAGCCACGTGCCCCCTAATGAA
TTAAACACAAACAGCGACGGAAGTTACACAAACGCCAGCACAAATTCAACCAGTGTCACATCATCTACACCAACAGTGGT
ATCC

Alignment

ORF - retro_hsap_4173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.25 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAWIKRKFGERPPPKRLTREAMRNYLKERGDQTVLILHAKVAQKSYGNEKRFFCP-PPCVYLMGSGWKKK
          MAWIKRKFG..PP.KRLTREAM.NYLK..GDQ.VL.LHAKV.QKSYGNEKR...P.PPCVYLMGSGWKK.
Retrocopy MAWIKRKFGKWPPFKRLTREAM*NYLKG*GDQIVLSLHAKVVQKSYGNEKRXXXP>PPCVYLMGSGWKKI

Parental  KEQMERDGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDI
          K.QM..DGCSEQ.SQP.AFIGIGNSDQEMQQLNLEGKNYCTAKTLYISD.DK.KHFMLSVK.FYGNSDDI
Retrocopy K*QMKCDGCSEQGSQPSAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDLDKQKHFMLSVKVFYGNSDDI

Parental  GVFLSKRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHASSQQW-GAFFI
          GVFLSK.....SKPSKKKQSLKNADLCIASG.KVALFNRL.SQTVSTRYLHVE.GNFH..S.Q..G..F.
Retrocopy GVFLSKS----SKPSKKKQSLKNADLCIASGKKVALFNRLLSQTVSTRYLHVERGNFH-ASSQQ>GEHFT

Parental  HLLDDDESEGEEFTVRDGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTALLDADDPVSQLHKCAFYLKD
          ..LDDD.SEGEEFTV.DGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQT.LLDADDPVSQLHKCAF.L.D
Retrocopy LFLDDDGSEGEEFTV*DGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTTLLDADDPVSQLHKCAFDLED

Parental  TERMYLCLSQERIIQFQATPCPKEPNKEMINDGASWTIISTDKAEYTFYEGMGPVLAPVTPVPVVESLQL
          TER.YLCLSQERIIQFQATPCPKEPNKE.INDGASW.IIST.KA..TFYE..GPVLA.V.P.PVVESL.L
Retrocopy TERKYLCLSQERIIQFQATPCPKEPNKEKINDGASWAIISTHKAKHTFYERVGPVLALVMPPPVVESLKL

Parental  NGGGDVAMLELTGQNFTPNLRVWFGDVEAETMYRCGESMLC-VVPDISAFREGWRWVRQPVQVPVTLVRN
          NGGGD..MLELTGQNFTPNL.VWFGDVEAE.MYRCGESML..VVPD.SAF.EGWR.V.QP.QV.VTLVRN
Retrocopy NGGGDEPMLELTGQNFTPNLQVWFGDVEAEAMYRCGESMLV<VVPDVSAF*EGWR*VQQPIQVSVTLVRN

Parental  DGIIYSTSLTFTYTPEPGPRPHCSAAGAILRANSSQVPPNESNTNSEGSYTNASTNSTSVTSSTATVVS
          DGIIYSTSLTFTYTPE.GPRPHCS.AGAIL.A.SS.VPPNE.NTNS.GSYTNASTNSTSVTSST.TVVS
Retrocopy DGIIYSTSLTFTYTPEAGPRPHCSVAGAILQASSSHVPPNELNTNSDGSYTNASTNSTSVTSSTPTVVS

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	243.92 RPM
bodymap2_adrenal	0.00 RPM	167.50 RPM
bodymap2_brain	0.00 RPM	162.25 RPM
bodymap2_breast	0.00 RPM	202.51 RPM
bodymap2_colon	0.00 RPM	252.87 RPM
bodymap2_heart	0.00 RPM	79.27 RPM
bodymap2_kidney	0.00 RPM	100.20 RPM
bodymap2_liver	0.00 RPM	31.71 RPM
bodymap2_lung	0.00 RPM	162.04 RPM
bodymap2_lymph_node	0.00 RPM	172.28 RPM
bodymap2_ovary	0.00 RPM	209.71 RPM
bodymap2_prostate	0.00 RPM	214.93 RPM
bodymap2_skeletal_muscle	0.00 RPM	91.59 RPM
bodymap2_testis	0.00 RPM	219.11 RPM
bodymap2_thyroid	0.00 RPM	112.95 RPM
bodymap2_white_blood_cells	0.00 RPM	223.63 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4173 was not detected

EST

No EST(s) were mapped for retro_hsap_4173 retrocopy.

TSS

No TSS is located nearby retro_hsap_4173 retrocopy 5' end.

Lab

retro_hsap_4173 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4173 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003602	1 retrocopy	retro_btau_1507,
Choloepus hoffmanni	ENSCHOG00000001582	4 retrocopies	retro_chof_1172, retro_chof_1278, retro_chof_2449, retro_chof_371,
Homo sapiens	ENSG00000168214	6 retrocopies	retro_hsap_4169, retro_hsap_4171, retro_hsap_4173 , retro_hsap_4174, retro_hsap_4256, retro_hsap_4316,
Gorilla gorilla	ENSGGOG00000004582	1 retrocopy	retro_ggor_2853,
Mus musculus	ENSMUSG00000039191	2 retrocopies	retro_mmus_2348, retro_mmus_2819,
Nomascus leucogenys	ENSNLEG00000016895	1 retrocopy	retro_nleu_2305,
Oryctolagus cuniculus	ENSOCUG00000013449	1 retrocopy	retro_ocun_1445,
Pan troglodytes	ENSPTRG00000015968	1 retrocopy	retro_ptro_2829,
Tursiops truncatus	ENSTTRG00000009022	2 retrocopies	retro_ttru_1151, retro_ttru_1593,