RetrogeneDB ID: retro_mmul_31

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214732597:669..1692(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000032376
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.4180
• Ensembl ID: ENSMMUG00000013929
• Aliases: None
• Description: immunoglobulin (CD79A) binding protein 1 [Source:RefSeq peptide;Acc:NP_001182718]

Sequence

>retro_mmul_31
ATGGCAGCTGCTGAAGACGAGTTTCTGCCGCCGCCGCGGCTCCCCGAGCTGTTCGATTCCAGCAAACAGCTTCTGGAAGA
AGTCGAAGGAGCGACTGAACCCACCGGTTCCCGGATAGTCCAGGAAAAGGTGTTAAAGGGCCTCGACCTCCTTCAGAAGG
TTGCCAAAATGTTATCGCAGCTCGACTTGTTTAGCCGAAATGAAGATTTGGAGGAGATTACTTCCACCGACCTGAAGTAC
CTGATGGTGCCAGCGTTTCAAGGAGCCCTCACCATGAAACAAGTCAACCCCAGTAAGCGTCTAGATCATTTGCAGCAGGC
TCGCGAACACTTTATAAAATACTTAACTCAGTGTCATTACTATCGTGTGGCCGAGTTTGAGCTACCCCAAACCAAGACCA
ACTCAGCTGAAAAAAACACTGCTATTACTTCCACGGTTTATCCTAGCCTCGTTGCTATGGCATCTCAAAGACAGGCTAAA
ATAGAGAGATACAAGCAGAAGAAGGAGTTGGAGCATAGGTTGTCTACAATGAAATCTGCTGTGGAAAGTGGTCAAGCAGA
TGATGAGCGTGTTCGTGAATATTATCTTCTTCACCTTCAGAGGTGGATTGATACCAGCTTAGAAGAGATTGAGAGCATTG
ATCAGGAAATAAAGATCCTGGGAGAGAAAGACTTTTCAAGAGAGGCATCCACTTCGAACTCATCTGGCCATGAGAGGCCT
CTAATAAAACCCTTCATTCTCACTCGGAACATGGCGCAAGCCAAAGTATTTGGCGCTGGTTATCCAAGTCTGGCTTCTAT
GACAGTGAGTGACTGGTATGATCAACATCAGAAACATGCAGTGTTACCAGATCAGGGAATAGCTAAGGCAACACCAGAAG
AATTCAGAAAAGCCACTCCGCAACAGAAAGATCAAGAAAAGGAGGAAGAGGATGATGAACAAACACTCCAAAGAGCTCGA
GAGTGGGATGACTGGAAGGACACCCACCCTAGGGGTTACGGCAACCGACAGAACATGGGCTAA

Alignment

ORF - retro_mmul_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.96 %
• Parental protein coverage: 99.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAEDELLLP-RLPELFETGKQLLDEVEVATEPAGSRIVQEKVFKGLDLLEKAAEMLSQLDLFSRNEDLEE
          AAEDE.L.P.RLPELF...KQLL.EVE.ATEP.GSRIVQEKV.KGLDLL.K.A.MLSQLDLFSRNEDLEE
Retrocopy AAEDEFLPPPRLPELFDSSKQLLEEVEGATEPTGSRIVQEKVLKGLDLLQKVAKMLSQLDLFSRNEDLEE

Parental  IASTDLKYLLVPAFQGALTMKQVNPSKRLDHLQRAREHFMNYLTQCHCYHVAEFELPKTKNNSAENHTAN
          I.STDLKYL.VPAFQGALTMKQVNPSKRLDHLQ.AREHF..YLTQCH.Y.VAEFELP.TK.NSAE..TA.
Retrocopy ITSTDLKYLMVPAFQGALTMKQVNPSKRLDHLQQAREHFIKYLTQCHYYRVAEFELPQTKTNSAEKNTAI

Parental  SSMAYPSLVAMASQRQAKIERYKQKKELEHRLSAMKSAVESGQADDERVREYYHLHLQRWIDISLEEIES
          .S..YPSLVAMASQRQAKIERYKQKKELEHRLS.MKSAVESGQADDERVREYY.LHLQRWID.SLEEIES
Retrocopy TSTVYPSLVAMASQRQAKIERYKQKKELEHRLSTMKSAVESGQADDERVREYYLLHLQRWIDTSLEEIES

Parental  IDQEIKILRERDSSREASTSNSSRQERPPVKPFILTRNTAQAKVFGAGYPSLATMTVSDWYEQHRKYGAL
          IDQEIKIL.E.D.SREASTSNSS..ERP..KPFILTRN.AQAKVFGAGYPSLA.MTVSDWY.QH.K...L
Retrocopy IDQEIKILGEKDFSREASTSNSSGHERPLIKPFILTRNMAQAKVFGAGYPSLASMTVSDWYDQHQKHAVL

Parental  PDQGIAKATPEEFRKAAQQQEEQEEKEEEDDEQTLHRAREWDDWKDTHPRGYGNRQNMG
          PDQGIAKATPEEFRKA..QQ..Q.EKEEEDDEQTL.RAREWDDWKDTHPRGYGNRQNMG
Retrocopy PDQGIAKATPEEFRKATPQQKDQ-EKEEEDDEQTLQRAREWDDWKDTHPRGYGNRQNMG

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	31.04 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	36.57 RPM
SRP007412_cerebellum	0.00 RPM	33.13 RPM
SRP007412_heart	0.00 RPM	39.10 RPM
SRP007412_kidney	0.23 RPM	34.86 RPM
SRP007412_liver	0.00 RPM	8.91 RPM
SRP007412_testis	51.98 RPM	18.32 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_31 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_31 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_31 has 0 orthologous retrocopies within eutheria group .

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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,