RetrogeneDB ID: retro_mmul_1853

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:124136470..124137766(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TRIP4
• Ensembl ID: ENSMMUG00000009882
• Aliases: None
• Description: activating signal cointegrator 1 [Source:RefSeq peptide;Acc:NP_001253149]

Sequence

>retro_mmul_1853
CAGTGCTTCCAAAAAGATGAAACTTTAGATGGGCAGAAATCAAGGGACCAGCTAAAGCTGGGTAGGAGGAAAGGGAGAGA
CAGACAGGAAGTTCCTGTATTTGCTGAACCTGACACAACTGCAGAGGTAAAACACCTTTTAATTTGCCCAAGGCATGAGA
GAACAGCAACTCCTTTAAGAGTAAGACAAAGTTTGTCAATTTACACACAAGAGAGGGACCCACAGGCTTGCAGTCTGCTC
CCGGGTTGCCATCCTTGTGATTGCCTGGGCCAGAAGTACAAGCTCATCAGTAGCTGTCTGATCTGTGGGCCTGTTGTTTG
TGAAAAAGAGGGTGCCAGCCCTTGCTTATTCTGTGTCACAACAGTATGTACTCATGAAGAACAGGATATTTTGCAGCATG
AGTCAAATGAGAGCCAGAAACTGCTAAAGAAGCTTATGCCATTGATGGAGAATTCTGGAAAGGTGGACAACTCTGCCAAG
GACTTTCTATGTCATTGAGAATTTCAAATTATGTCTGGTCTGGAGAAGGATATCAAGCACAAAGACAGGCTGTTAGAGTT
GCACAGAGCTAGTTTTCAAAGGACCCAAGTCATTGATGCTGATCAGATTTTTTTGCCAGTGACTCTAACCAGTGGTTTTC
CAAACTTGAGTGGGAAACCAAATGAGAAGCAAGAAGAGGAGCTGAGAGAACTTCGACATGCCTCTTGACTCTCTAAGAAG
GTCACCATTGAGTTTACAGCAGGAAGATCCTGGAAGAAGAAAATCCATTAGCAGAATATCACAGCAGACTAGACGAGACA
ATACAGGCCATTGCTAAGGAAACCTTGAATGAGACACTGACCCCATTTTATATATCTCCTGAAGAGCCTTTGGGAGTTCT
GGTAAATCTCAGCACATACCAGTCCCCTCCCCAGTGGGTTGACCATGCAGGTGCAGCCTCACAGAATAAGGCTTTCCATT
CAGCAGGATTGGGACTGGAATTCAACTCATTTCAGTACTTCTTGTGAATCCAGGACCAAGACTTTCAGGGAGGTTTGACA
GTGGCTCATGTCTCTCTATACATCAGGCCTGGGTTTCTCAGCTTGTTAGAGGGATTAGAAAATGATGGAGTGCAGATCCT
GGTATATCTCCCACAGAGGACAACTTTGGATAGCAGTCGTAGCCAAAACCTCCCTCTGCCTTCAAGAAGTCTCAGAACTC
CAGGTTACGTATCATCTTCTTCATGGGAAAGATGTGGAATTCCCCAGTGACTATCCATCAGGTTGTCTTTTGGGCTGTCT
GGACCTAATTGCTTGT

Alignment

ORF - retro_mmul_1853 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.62 %
• Parental protein coverage: 74.35 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  QCFKKDEILDGQKSGDHLKRGRKKGRNRQEVPAFTEPDTTAEVK-TPFDLAKAQENSNSVKKKTKFVNLY
          QCF.KDE.LDGQKS.D.LK.GR.KGR.RQEVP.F.EPDTTAEVK.TPF.L.KA.ENSNS.K.KTKFVNL.
Retrocopy QCFQKDETLDGQKSRDQLKLGRRKGRDRQEVPVFAEPDTTAEVK<TPFNLPKA*ENSNSFKSKTKFVNLH

Parental  TREGQD-RLAV-LLPGRHPCDCLGQKHKLINNCLICGRIVCEQEGSGPCLFCGTLVCTHEEQDILQRDSN
          TREG...RLAV.LLPG.HPCDCLGQK.KLI..CLICG..VCE.EG..PCLFC.T.VCTHEEQDILQ..SN
Retrocopy TREGPT<RLAV<LLPGCHPCDCLGQKYKLISSCLICGPVVCEKEGASPCLFCVTTVCTHEEQDILQHESN

Parental  KSQKLLKKLMSGVENSGKVDISTKDLLPHQELRIKSGLEKAIKHKDKLLEFDRTSIRRTQVIDDE-SDYF
          .SQKLLKKLM...ENSGKVD.S.KD.L.H.E..I.SGLEK.IKHKD.LLE..R.S..RTQVID...SD.F
Retrocopy ESQKLLKKLMPLMENSGKVDNSAKDFLCH*EFQIMSGLEKDIKHKDRLLELHRASFQRTQVIDAD<SDFF

Parental  ASDSNQWLSKLERETL-QKREEELRELRHASRLSKKVTIDFAG-RKILEEENSLAEYHSRLDETIQAIAN
          ASDSNQW.SKLE.ET...K.EEELRELRHAS.LSKKVTI.F...RKILEEEN.LAEYHSRLDETIQAIA.
Retrocopy ASDSNQWFSKLEWETK>EKQEEELRELRHAS*LSKKVTIEFTA<RKILEEENPLAEYHSRLDETIQAIAK

Parental  GTLNQPLTKLDRSSEEPLGVLVNPNMYQSPPQWVDHTGAASQKKAFRSSGLGLEFNSLQHQLRIQDQEFQ
          .TLN..LT....S.EEPLGVLVN...YQSPPQWVDH.GAASQ.KAF.S.GLGLEFNS.Q..L.IQDQ.FQ
Retrocopy ETLNETLTPFYISPEEPLGVLVNLSTYQSPPQWVDHAGAASQNKAFHSAGLGLEFNSFQYFL*IQDQDFQ

Parental  EG-FDGGWCLSIHQPWASL-LVRGI-KRVEGRSWYTPHRGRLWIAATAKKP-SPQEVSELQATYRLLRGK
          .G.FD.G.CLSIHQ.W.S..L..G..K..E.RSWY..HRG.LWIA..AK.....QEVSELQ.TY.LL.GK
Retrocopy GG<FDSGSCLSIHQAWVSQ>LLEGL>KMMECRSWYISHRGQLWIAVVAKTSLCLQEVSELQVTYHLLHGK

Parental  DVEFPNDYPSGCLLGCVDLTDC
          DVEFP.DYPSGCLLGC.DL..C
Retrocopy DVEFPSDYPSGCLLGCLDLIAC

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	6.84 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.65 RPM
SRP007412_cerebellum	0.00 RPM	7.04 RPM
SRP007412_heart	0.00 RPM	7.13 RPM
SRP007412_kidney	0.12 RPM	12.79 RPM
SRP007412_liver	0.00 RPM	4.12 RPM
SRP007412_testis	0.00 RPM	26.42 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1853 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1853 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1853 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000032766	1 retrocopy	retro_cjac_2382,
Macaca mulatta	ENSMMUG00000009882	1 retrocopy	retro_mmul_1853 ,
Oryctolagus cuniculus	ENSOCUG00000002322	1 retrocopy	retro_ocun_663,