RetrogeneDB ID: retro_mmus_2819

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:46529353..46530799(-)
• Located in intron of: ENSMUSG00000039419

Retrocopy information

• Ensembl ID: ENSMUSG00000079575
• 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_2819
TATAGGAAGTTTGGTGAGCGGCCTCCACCCAAACGACTCACTAGGGAAGCTATGCGAAATTATTTAAAAGAACGAGGGGA
TCAAACAGTGCTCATTCTTCATGCAAAAGTTGCACAGAAGTCTTACGGAAATGAAAAACGATTTTTTTGCCCTCCTCCTT
GTGTGTATCTTATGGGCAGTGGTTGGAAGAAAAAAAAAGAGCAAATGGAACGAGATGGATGTTCTGAACAAGAGTCTCAA
CCCTGTGCGTTTATTGGAATAGGAAACAGTGACCAAGAAATGCAGCAGCTGAACTTGGAAGGGAAGAACTACTGCACAGC
CAAAACATTGTACATATCTGATTCAGACAAGAGAAAACATTTCATGTTGTCTGTAAAGATGTTCTATGGCAACAGCGATG
ACATTGGTGTGTTCCTCAGCAAGCGGATAAAGGTCATCTCCAAACCCTCCAAAAAGAAGCAGTCACTGAAGAATGCTGAC
TTGTGCATTGCTTCAGGAACGAAGGTGGCACTGTTCAATCGCCTTCGGTCCCAGACAGTTAGTACCAGGTACCTGCATGT
AGAAGGAGGGAATTTCCACGCCAGTTCACAACAGTGGGGAGCATTTTACATCCATCTCTTGGACGACGACGAGTCGGAAG
GAGAGGAGTTCACAGTTAGAGATGGCTACATCCATTACGGGCAGACTGTCAAGCTTGTGTGCTCAGTGACTGGCATGGCA
CTCCCAAGATTGATAATTAGGAAAGTTGATAAGCAGACGGCATTACTGGATGCAGACGACCCTGTATCACAACTCCACAA
ATGTGCATTTTACCTTAAGGATACAGAAAGAATGTACTTGTGCCTTTCTCAAGAAAGAATAATCCAATTTCAGGCCACTC
CATGTCCAAAAGAACAAAATAAGGAAATGATAAACGATGGAGCTTCCTGGACAATCATTAGCACAGACAAGGCAGAATAC
ACGTTCTATGAGGGAATGGGCCCCGTCCTTGCCCCAGTCACCCCTGTGCCTGTCGTAGAAAGTCTTCAGTTGAATGGCGG
CGGGGACGTAGCAATGCTTGAACTTACAGGACAAAACTTTACTCCAAATTTACGAGTGTGGTTTGGGGATGTAGAAGCCG
AAACAATGTACAGATGTGGAGAGAGCATGCTCTGTGTGGTCCCAGACATTTCTGCATTCCGGGAAGGTTGGAGATGGGTC
CGCCAGCCAGTCCAGGTTCCAGTGACTTTGGTCCGAAATGACGGGGTCATTTACTCCACCAGCCTTACCTTCACCTACAC
ACCAGAGCCAGGGCCGAGGCCACACTGCAGCGCTGCAGGAGCGATTCTCAGAGCCAACTCCAGCCAAGTGCCCTCCAATG
AGTCAAACACAAACAGCGAGGGGAATTACACAAATGCCAGCACAAATTCTACCAGTGTCACATCGTCCACAGCAACCGTG
GTGTCC

Alignment

ORF - retro_mmus_2819 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.38 %
• Parental protein coverage: 99.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YRKFGERPPPKRLTREAMRNYLKERGDQTVLILHAKVAQKSYGNEKRFFCPPPCVYLMGSGWKKKKEQME
          YRKFGERPPPKRLTREAMRNYLKERGDQTVLILHAKVAQKSYGNEKRFFCPPPCVYLMGSGWK...EQME
Retrocopy YRKFGERPPPKRLTREAMRNYLKERGDQTVLILHAKVAQKSYGNEKRFFCPPPCVYLMGSGWKXXXEQME

Parental  RDGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIGVFLS
          RDGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIGVFLS
Retrocopy RDGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIGVFLS

Parental  KRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHASSQQWGAFYIHLLDDD
          KRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHASSQQWGAFYIHLLDDD
Retrocopy KRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHASSQQWGAFYIHLLDDD

Parental  ESEGEEFTVRDGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTALLDADDPVSQLHKCAFYLKDTERMYL
          ESEGEEFTVRDGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTALLDADDPVSQLHKCAFYLKDTERMYL
Retrocopy ESEGEEFTVRDGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTALLDADDPVSQLHKCAFYLKDTERMYL

Parental  CLSQERIIQFQATPCPKEQNKEMINDGASWTIISTDKAEYTFYEGMGPVLAPVTPVPVVESLQLNGGGDV
          CLSQERIIQFQATPCPKEQNKEMINDGASWTIISTDKAEYTFYEGMGPVLAPVTPVPVVESLQLNGGGDV
Retrocopy CLSQERIIQFQATPCPKEQNKEMINDGASWTIISTDKAEYTFYEGMGPVLAPVTPVPVVESLQLNGGGDV

Parental  AMLELTGQNFTPNLRVWFGDVEAETMYRCGESMLCVVPDISAFREGWRWVRQPVQVPVTLVRNDGVIYST
          AMLELTGQNFTPNLRVWFGDVEAETMYRCGESMLCVVPDISAFREGWRWVRQPVQVPVTLVRNDGVIYST
Retrocopy AMLELTGQNFTPNLRVWFGDVEAETMYRCGESMLCVVPDISAFREGWRWVRQPVQVPVTLVRNDGVIYST

Parental  SLTFTYTPEPGPRPHCSAAGAILRANSSQVPSNESNTNSEGNYTNASTNSTSVTSSTATVVS
          SLTFTYTPEPGPRPHCSAAGAILRANSSQVPSNESNTNSEGNYTNASTNSTSVTSSTATVVS
Retrocopy SLTFTYTPEPGPRPHCSAAGAILRANSSQVPSNESNTNSEGNYTNASTNSTSVTSSTATVVS

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	0.42 RPM	16.21 RPM
SRP007412_cerebellum	1.35 RPM	13.42 RPM
SRP007412_heart	0.09 RPM	16.25 RPM
SRP007412_kidney	1.56 RPM	13.11 RPM
SRP007412_liver	0.46 RPM	5.30 RPM
SRP007412_testis	0.87 RPM	4.76 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2819 was not detected

EST

No EST(s) were mapped for retro_mmus_2819 retrocopy.

TSS

No TSS is located nearby retro_mmus_2819 retrocopy 5' end.

Lab

retro_mmus_2819 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2819 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,