RetrogeneDB ID: retro_mmus_169

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:138657412..138658444(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000046717
• Aliases: Igbp1b, alpha4-b
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Igbp1
• Ensembl ID: ENSMUSG00000031221
• Aliases: Igbp1, AI115586, AI662457, AW208785, C81413, Pc52, Tap42, p52
• Description: immunoglobulin (CD79A) binding protein 1 [Source:MGI Symbol;Acc:MGI:1346500]

Sequence

>retro_mmus_169
ATGGCGTCGTTTATGGAGGAGATGCAGAAGCCGAAGCTCCGGGAGCTGTTGGAAACCGGCATACAACTTCTGGAGGAGGT
GGAAGCTGCGACCCAACCCACAGGCTCCAAGCCAATCCAGGAAAAGGTGAGGGAGGCCTTGAAGCTCCTGGAGAAGGCCT
CGGACATGTTATCGCAGCTCGATTTGTTCAGCAGGAACGAAGATTGGGAAGAGATTGCTTCCGCTGACCTAAAGTACCTG
ATGCTCCCGGCCCTGAAGGGCGCGCTGACGCTGAAGCTGGTGGGCAGCAGCAAACGCCTAGGCCTCCTGCAGGATGCTCG
AGAACACTTCATGAACTTCCTAACCCAGACCCACAGCTACCATGTGGCTGATTTTCAGCTGCCCTGGGCCCAGAGCAGCT
CAACGGAAGGCAACCCCGCTGCCACCTCTGATGCCCAGGAGCAAAACCTGGTTGCCATGGCATCCCAGAGGCAGACCAAA
ATCCAGAGGTACAAGCAGAAGAAGGCGGTGGAGCAGAGGCTGTCTTCTCTGAAATCGGCAGTGGAGAGCGGCCAGGCTGA
CGATGAGCGTGTCAGGGAGTATTACCTCCTTCAGCTTCGTAGGTGGATTAGCATCAGCCTGGATGAGATCGAGAACATCG
AACAGGAGATAGAGATCCTGAGGGAAAGAGACTCCTTAGGTGAGACATCAGCATCTCGCTCATCTCCTCAGGAGAGGCCT
CCACTAAAACCCTTCGTCCTCACTCGAAGTGTTGCCCAAGCACAAGTGTTTGGAGCTGGGTACCCAAGTCTGGCAACTAT
GACCGTGAATGACTGGTACGAGCAGCGCCAGAAAAATGAGGTCTCACCAACTCTTCAGGAAGCAGAAAAGCAGGCACCAC
CATCTGAGACTTTCACTGTATCTGAGAAGGAAGAGCCAGACCTGGAGCAAAAGGAAGATGAAGATGAGAATGCCCTCCAC
AGGATGCAGGAGTGGGATGACTGGAAGGACACTCATCCTAGGGGATATGGCAACCGACAGAACATGGGCTAA

Alignment

ORF - retro_mmus_169 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.99 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASEDELLLPRLPELFETSKKLLEDVEVATEPTGSRTIQDKVSKGLELLEKAAGMLSQLDLFSRNEDLE
          MA....E...P.L.EL.ET...LLE.VE.AT.PTGS..IQ.KV...L.LLEKA..MLSQLDLFSRNED.E
Retrocopy MASFMEEMQKPKLRELLETGIQLLEEVEAATQPTGSKPIQEKVREALKLLEKASDMLSQLDLFSRNEDWE

Parental  EIASTDLKYLMVPALQGALTMKQVNPSKRLDHLQRAREHFVHFLTQCHCYHVAEFQLPQTKTNSAENNTA
          EIAS.DLKYLM.PAL.GALT.K.V..SKRL..LQ.AREHF..FLTQ.H.YHVA.FQLP.....S.E.N.A
Retrocopy EIASADLKYLMLPALKGALTLKLVGSSKRLGLLQDAREHFMNFLTQTHSYHVADFQLPWAQSSSTEGNPA

Parental  SSSMAYP-NLVAMASQRQAKIERYKQKKEVEHRLSALKSAVESGQADDERVREYHLLHLRRWIAVSLEEL
          ..S.A...NLVAMASQRQ.KI.RYKQKK.VE.RLS.LKSAVESGQADDERVREY.LL.LRRWI..SL.E.
Retrocopy ATSDAQEQNLVAMASQRQTKIQRYKQKKAVEQRLSSLKSAVESGQADDERVREYYLLQLRRWISISLDEI

Parental  ESIDQEIKILKEKDSPREETACHSSLPEKPPMKPFILTRNKAQAKVFGTGYPSLATMTVSDWYEQHQKYG
          E.I.QEI.IL.E.DS..E..A..SS..E.PP.KPF.LTR..AQA.VFG.GYPSLATMTV.DWYEQ.QK..
Retrocopy ENIEQEIEILRERDSLGETSASRSSPQERPPLKPFVLTRSVAQAQVFGAGYPSLATMTVNDWYEQRQKNE

Parental  VLPDRGIAK---PASADFQRAAQQQEDQEQKDEESEEKALHRMREWDDWKDTHPRGYGNRQNMG
          V.P....A....P.S..F........D.EQK..E..E.ALHRM.EWDDWKDTHPRGYGNRQNMG
Retrocopy VSPTLQEAEKQAPPSETFTVSEKEEPDLEQKEDE-DENALHRMQEWDDWKDTHPRGYGNRQNMG

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	0.28 RPM	29.55 RPM
SRP007412_cerebellum	0.00 RPM	37.52 RPM
SRP007412_heart	0.00 RPM	33.03 RPM
SRP007412_kidney	0.00 RPM	58.50 RPM
SRP007412_liver	0.00 RPM	47.74 RPM
SRP007412_testis	31.06 RPM	5.17 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_169 was not detected

EST

No EST(s) were mapped for retro_mmus_169 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_119911	1055 libraries	12 libraries	1 library	0 libraries	4 libraries

The graphical summary, for retro_mmus_169 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_169 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_169 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_311

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007797	1 retrocopy	retro_btau_215,
Choloepus hoffmanni	ENSCHOG00000013654	3 retrocopies	retro_chof_1523, retro_chof_2206, retro_chof_438,
Callithrix jacchus	ENSCJAG00000012525	6 retrocopies	retro_cjac_111, retro_cjac_1225, retro_cjac_2278, retro_cjac_2968, retro_cjac_3417, retro_cjac_47,
Cavia porcellus	ENSCPOG00000010797	1 retrocopy	retro_cpor_44,
Dasypus novemcinctus	ENSDNOG00000014731	5 retrocopies	retro_dnov_1160, retro_dnov_2029, retro_dnov_2340, retro_dnov_2380, retro_dnov_678,
Echinops telfairi	ENSETEG00000003397	1 retrocopy	retro_etel_1637,
Felis catus	ENSFCAG00000029688	1 retrocopy	retro_fcat_23,
Homo sapiens	ENSG00000089289	5 retrocopies	retro_hsap_1317, retro_hsap_1848, retro_hsap_2766, retro_hsap_2919, retro_hsap_3059,
Gorilla gorilla	ENSGGOG00000027795	2 retrocopies	retro_ggor_112, retro_ggor_2020,
Myotis lucifugus	ENSMLUG00000004179	1 retrocopy	retro_mluc_316,
Macaca mulatta	ENSMMUG00000013929	2 retrocopies	retro_mmul_1545, retro_mmul_31,
Mus musculus	ENSMUSG00000031221	1 retrocopy	retro_mmus_169 ,
Nomascus leucogenys	ENSNLEG00000000747	5 retrocopies	retro_nleu_1399, retro_nleu_1653, retro_nleu_2334, retro_nleu_671, retro_nleu_828,
Otolemur garnettii	ENSOGAG00000011797	1 retrocopy	retro_ogar_110,
Pongo abelii	ENSPPYG00000020435	4 retrocopies	retro_pabe_1099, retro_pabe_1451, retro_pabe_2245, retro_pabe_2533,
Pan troglodytes	ENSPTRG00000021990	5 retrocopies	retro_ptro_1233, retro_ptro_1873, retro_ptro_1973, retro_ptro_1982, retro_ptro_901,
Pteropus vampyrus	ENSPVAG00000005483	1 retrocopy	retro_pvam_1462,
Rattus norvegicus	ENSRNOG00000026267	1 retrocopy	retro_rnor_311,
Tarsius syrichta	ENSTSYG00000006214	2 retrocopies	retro_tsyr_1537, retro_tsyr_2131,