RetrogeneDB ID: retro_mmul_1832

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:56593891..56594879(-)
• Located in intron of: ENSMMUG00000029604

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3731
• Ensembl ID: ENSMMUG00000004122
• Aliases: None
• Description: Microtubule-associated protein [Source:UniProtKB/TrEMBL;Acc:F6R387]

Sequence

>retro_mmul_1832
GAAAGATCAAGAGGGCTACACCATGCTCCAAGACCAAGAGGGTGACACGGACGCTGGCCTGAAAGCTGAAGAAGCAGGCA
TTGGAGACACCCCCAGCCTGAAAGATGAAGCTGCTGGTCACGTGACCGAAGCTCACTAGATCAGTCAAAGCAAAGACGGA
ACTGGAAGCGATGACAAAAAAGCCAAGGGGGCTGATAGTAAAACGAAGATCGCCACACCCAGGGGAGCGGCCCCCCCAGG
CCAGAAAATCCAGGCCAACGCCACCAGGATTCCAGCAAAAACCCCGCCCGCCCCAAAGACACCACCCAGTTCTGGTGAAC
CTCCAAAATCAGGGGATCGTAGCGGCTACAGCAGCCTCGGCTCCCCGGGCACTCCTGGCAGCCGCTCCCGCATCCCGTCC
CTTCCAACCCCTCCAGCCCGGGAGCCCAAGAAGGTGGCGGTGGTCCGTACTCCACCCAAATCGCCGTCTTCCGCTAACAG
CCGCCTGCAGACCGCCCCCGTGCCCATGCCAGACCTGAAGAACGTCAAGTCCAAGATCGACTCCACTGAGAACCTGAAGC
ATCAGCCGGGAGGCGGGAAGGTGCAAATAGTCTACAAATCAGTTGACCTGAGCAAGGTGACCTCCAAGTGTGGCTCATTA
GGCAACATCCATCATAAACCAGGAGGTGGCCAGGTGGAAGTAAAATCTGAGAAGCTGGACTTCAAGGACAGAGTCCAGTC
GAAGATCGGGTCCCTGGACAATATCACTCATGTCCCTGGCGGAGGAAATAAAAAGATTGAAACCCACAAGCTGACCTTCC
GCGAGAACGCCAAAGCCAAGACAGACCACCGGGTGGAAATCGTGAACAAGTCGCCGGTGGTGTCTGGGGACACGTCTCCA
TGGCACCTCAGCAATGTCTCCTCCACCGGCAGCATCGACATGGTAGACTCGCCCCAGCTCGCCACGCTAGCCGTCGAGGT
GTCTGCCTCCCTGGCCAAGCAGGGTTTG

Alignment

ORF - retro_mmul_1832 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.58 %
• Parental protein coverage: 80.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERAPGEQAAAQPHM-EIPEGTTAEEAGIGDTPSLEDEAAGHVTQARMVSKSKDGTGSDDKKAKGADGKTK
          ER..G...A..P.......G..AEEAGIGDTPSL.DEAAGHVT.A...S.SKDGTGSDDKKAKGAD.KTK
Retrocopy ERSRGLHHAPRPRG>DTDAGLKAEEAGIGDTPSLKDEAAGHVTEAH*ISQSKDGTGSDDKKAKGADSKTK

Parental  IATPRGAAPPGQKGQANATRIPAKTPPAPKTPPSSGEPPKSGDRSGYSSPGSPGTPGSRSRTPSLPTPPA
          IATPRGAAPPGQK.QANATRIPAKTPPAPKTPPSSGEPPKSGDRSGYSS.GSPGTPGSRSR.PSLPTPPA
Retrocopy IATPRGAAPPGQKIQANATRIPAKTPPAPKTPPSSGEPPKSGDRSGYSSLGSPGTPGSRSRIPSLPTPPA

Parental  REPKKVAVVRTPPKSPSSAKSRLQTAPVPMPDLKNVKSKIGSTENLKHQPGGGKVQIVYKPVDLSKVTSK
          REPKKVAVVRTPPKSPSSA.SRLQTAPVPMPDLKNVKSKI.STENLKHQPGGGKVQIVYK.VDLSKVTSK
Retrocopy REPKKVAVVRTPPKSPSSANSRLQTAPVPMPDLKNVKSKIDSTENLKHQPGGGKVQIVYKSVDLSKVTSK

Parental  CGSLGNIHHKPGGGQVEVKSEKLDFKDRVQSKIGSLDNITH--SSGQRLIETHKLTFRENAKAKTDHGAE
          CGSLGNIHHKPGGGQVEVKSEKLDFKDRVQSKIGSLDNITH....G...IETHKLTFRENAKAKTDH..E
Retrocopy CGSLGNIHHKPGGGQVEVKSEKLDFKDRVQSKIGSLDNITHVPGGGNKKIETHKLTFRENAKAKTDHRVE

Parental  IVYKSPVVSGDTSPRHLSNVSSTGSIDMVDSPQLATLADEVSASLAKQGL
          IV.KSPVVSGDTSP.HLSNVSSTGSIDMVDSPQLATLA.EVSASLAKQGL
Retrocopy IVNKSPVVSGDTSPWHLSNVSSTGSIDMVDSPQLATLAVEVSASLAKQGL

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	11.54 RPM	55.69 RPM
SRP007412_brain_prefrontal_cortex	20.63 RPM	146.92 RPM
SRP007412_cerebellum	10.98 RPM	43.98 RPM
SRP007412_heart	0.71 RPM	9.77 RPM
SRP007412_kidney	1.64 RPM	9.04 RPM
SRP007412_liver	0.04 RPM	0.95 RPM
SRP007412_testis	3.20 RPM	2.49 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1832 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1832 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1832 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000004122	1 retrocopy	retro_mmul_1832 ,