RetrogeneDB ID: retro_mmus_2348

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:49350523..49351530(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081770
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rbpj
• Ensembl ID: ENSMUSG00000039191
• Aliases: Rbpj, AI843960, CBF1, Igkjrb, Igkrsbp, RBP-J, RBP-J kappa, RBPjk, Rbpsuh
• Description: recombination signal binding protein for immunoglobulin kappa J region [Source:MGI Symbol;Acc:MGI:96522]

Sequence

>retro_mmus_2348
CCCTCCAGTTTTCCTCAGTCTCCACATAAGTCCCAGAGGGTGCATCCCACAACCCGGATATCCAGAGCTCTCCCCATAGA
CTACTTGGAGGGCTCGCCCAAAAAGGAACAGCCTGCACATTCTTCATCATCGGGGACACTTGGTGAAAGGCCTCCACCTA
AATGACTCAACAGGGAAGCTATCAGAAATTACTTAAAAGAATGAGGGAATCAAACAGTACTCATTCTTCATGCAAACATT
GCGCAGAAGTTGTACAGAAATGAAAAACTTTTTTTTTTTTGCCCTCCTCCTTGTGTTTATCTTATGGGCAGTGGTTTGAA
GAAAAACAGAAAAAGAACAAATGGAACGAGATGATTGTTCTCAACAAACCCTGTGAGTTTATTGGAACAGGAAATAGTGA
CCAAGAAATGCAGCAGCTGAACTTGGAAGGGAAGAACTACTGTACAGCCAAAACATTGTACATACCTGATTCAGACAAGA
GAAAGCATTTCATGTTGTCTGTAAAGATGTTCTATGGCAACAGTGATGACACTGGTGTGTTCCTCAGCAAGCAGATAAAG
GTCATCTCCAAACCCTCCAAAAAGAAGCAGTCATTGAAAAATGCTGGCTTGTGAATTGCCTCGGGAATGAAGGTGGCACT
GTTCAATTGCATTACACCCCAGACAGTTAGTACCAGATACCTGCATGTAGAAGGAGGTAATTTCCACTCCAGTTAACAAC
AGTGGGGAGCATTTTACATTCATCTCCTGGGCGATGATGAGCCAGAAGGAGAAGAGTACATAGTTAGTGATGGCTACATC
CATTATGGACAGAGTGTCAGGCTTGCGTGCTCAGTGACTGGCATGGCGCTCCCAAGATTGATAATTAGGGAAGTTGATAA
GCAGACAGCATTACTGGATGCAGACAACCCTGTATCACAGCTCCACAAATGTGCATTTTACCTTAATGATACAGAAAAAA
TGTACTTGTGCCTTTCGAAAGAAAGAATATTCTAATTTGAGGCTACG

Alignment

ORF - retro_mmus_2348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.29 %
• Parental protein coverage: 63.88 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSGFPQSPRTSPRARPKTRITGALPMDYSEGLSAEERPAHAPSAGKFGERPPPKRLTREAMRNYLKERGD
          PS.FPQSP..S.R..P.TRI..ALP.DY.EG....E.PAH..S.G..GERPPPK.L.REA.RNYLKE.G.
Retrocopy PSSFPQSPHKSQRVHPTTRISRALPIDYLEGSPKKEQPAHSSSSGTLGERPPPK*LNREAIRNYLKE*GN

Parental  QTVLILHAKVAQKSYGNEKRFFCPPP-CVYLMGSGWKKKKEQMERDGCSEQESQPCAFIGIGNSDQEMQQ
          QTVLILHA..AQK.Y.NEK.....PP....L....W...K..............PC.FIG.GNSDQEMQQ
Retrocopy QTVLILHANIAQKLYRNEKXXXXXPP<SLCLSYGQWFEEKQKKNKWNEMIVLNKPCEFIGTGNSDQEMQQ

Parental  LNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIGVFLSKRIKVISKPSKKKQSLKNADLCIASG
          LNLEGKNYCTAKTLYI.DSDKRKHFMLSVKMFYGNSDD.GVFLSK.IKVISKPSKKKQSLKNA.L.IASG
Retrocopy LNLEGKNYCTAKTLYIPDSDKRKHFMLSVKMFYGNSDDTGVFLSKQIKVISKPSKKKQSLKNAGL*IASG

Parental  TKVALFNRLRSQTVSTRYLHVEGGNFHASSQQWGAFYIHLLDDDESEGEEFTVRDGYIHYGQTVKLVCSV
          .KVALFN....QTVSTRYLHVEGGNFH.S.QQWGAFYIHLL.DDE.EGEE..V.DGYIHYGQ.V.L.CSV
Retrocopy MKVALFNCITPQTVSTRYLHVEGGNFHSS*QQWGAFYIHLLGDDEPEGEEYIVSDGYIHYGQSVRLACSV

Parental  TGMALPRLIIRKVDKQTALLDADDPVSQLHKCAFYLKDTERMYLCLSQERIIQFQAT
          TGMALPRLIIR.VDKQTALLDAD.PVSQLHKCAFYL.DTE.MYLCLS.ERI..F.AT
Retrocopy TGMALPRLIIREVDKQTALLDADNPVSQLHKCAFYLNDTEKMYLCLSKERIF*FEAT

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	0.00 RPM	16.21 RPM
SRP007412_cerebellum	0.00 RPM	13.42 RPM
SRP007412_heart	0.00 RPM	16.25 RPM
SRP007412_kidney	0.10 RPM	13.11 RPM
SRP007412_liver	0.00 RPM	5.30 RPM
SRP007412_testis	0.00 RPM	4.76 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2348 was not detected

EST

No EST(s) were mapped for retro_mmus_2348 retrocopy.

TSS

No TSS is located nearby retro_mmus_2348 retrocopy 5' end.

Lab

retro_mmus_2348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2348 has 0 orthologous retrocopies within eutheria group .

---

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,