RetrogeneDB ID: retro_mmus_3160

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:105110676..105111421(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mapre1
• Ensembl ID: ENSMUSG00000027479
• Aliases: Mapre1, 5530600P05Rik, AI462499, AI504412, AW260097, BIM1p, D2Ertd459e, Eb1
• Description: microtubule-associated protein, RP/EB family, member 1 [Source:MGI Symbol;Acc:MGI:891995]

Sequence

>retro_mmus_3160
CTGGCTTGGAGCAATGAATCTCTGTAGTTGAATCTGACAAAGATAAAACAGTTGTGTTCAGGGGCTGTATACTGTCAGTT
TATGGACATGCTCTTCCCTGACTCCATTGCCTTGAAGAAAATGAAATTCCAAGCTAAGTTAGAACATGAATATATCCAAA
ACTTCAAAATATTACAAGCAGGCTTCAAGAGGCTGGGTGTTGACAAAATAATCCCTGTGGCTAAATTAGTAAAAGGAAAG
TTTCAGGACAATTTTGAGTTTGTTCAATGGTTCAAGAAGTTTTTTGATGCAAGTTATAATGGAAAAGAGTATGATCCTGT
AGCTGCCAGACAAGGTCAAGAAACTGCAGTGGCTCCTTCTCCTGTCACTCCAGCTTTGAGTAAACCGAAGAAACCTCTTG
GGTCCAGTAGTGCAGCCCTACAAAGACCCATTACAACATAGAGGACTACTGCAGCTCCTAAGGCTGGCCCAGGGATGATG
AGAAAGAATCCTGTTGTGGGTAATGGAGATGATGAAGCAGCTGTATTGATTCAGCGGGTCAAAGTATTGAAGCGTATACT
GTTGAAGACTTGGAGAAGGAGAGAAACTTCTACTTCATAAAGCTAAGAAACATTGAACTGATTTGCCAGGACAATGAGGG
GGGAAATGGCCCTGTACTGCAGAGGATTGTAGATATTCTTTATGCCACAGATGAAGGCTTTGTGATACCTGATGAAGGGG
CCCACAGGAGAAACAAGAAGAGTAT

Alignment

ORF - retro_mmus_3160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.67 %
• Parental protein coverage: 92.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LAWINESLQLNLTKIEQLCSGAAYCQFMDMLFPGSIALKKVKFQAKLEHEYIQNFKILQAGFKRMGVDKI
          LAW.NESL.LNLTKI.QLCSGA.YCQFMDMLFP.SIALKK.KFQAKLEHEYIQNFKILQAGFKR.GVDKI
Retrocopy LAWSNESL*LNLTKIKQLCSGAVYCQFMDMLFPDSIALKKMKFQAKLEHEYIQNFKILQAGFKRLGVDKI

Parental  IPVDKLVKGKFQDNFEFVQWFKKFFDANYDGKEYDPVAARQGQETAVAPSLVAPALSKPKKPLGSSTAAP
          IPV.KLVKGKFQDNFEFVQWFKKFFDA.Y.GKEYDPVAARQGQETAVAPS.V.PALSKPKKPLGSS.AA.
Retrocopy IPVAKLVKGKFQDNFEFVQWFKKFFDASYNGKEYDPVAARQGQETAVAPSPVTPALSKPKKPLGSSSAAL

Parental  QRPIATQRTTAAPKAGPGMVRKNPGVGNG-DDEAAELMQQVKVLKL-TVEDLEKERDFYFGKLRNIELIC
          QRPI.T.RTTAAPKAGPGM.RKNP.VGNG.D..A.............TVEDLEKER.FYF.KLRNIELIC
Retrocopy QRPITT*RTTAAPKAGPGMMRKNPVVGNGDDEAAVLIQRVKVLKRI<TVEDLEKERNFYFIKLRNIELIC

Parental  QENEGENDPVLQRIVDILYATDEGFVIPDEG-GPQEEQEEY
          Q.NEG.N.PVLQRIVDILYATDEGFVIPDEG.GPQE.QEEY
Retrocopy QDNEGGNGPVLQRIVDILYATDEGFVIPDEG<GPQEKQEEY

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	75.70 RPM
SRP007412_cerebellum	0.00 RPM	52.41 RPM
SRP007412_heart	0.03 RPM	62.26 RPM
SRP007412_kidney	0.00 RPM	78.35 RPM
SRP007412_liver	0.00 RPM	30.01 RPM
SRP007412_testis	0.00 RPM	52.42 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3160 was not detected

EST

No EST(s) were mapped for retro_mmus_3160 retrocopy.

TSS

No TSS is located nearby retro_mmus_3160 retrocopy 5' end.

Lab

retro_mmus_3160 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3160 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013238	3 retrocopies	retro_amel_1187, retro_amel_1436, retro_amel_848,
Canis familiaris	ENSCAFG00000007306	13 retrocopies	retro_cfam_1338, retro_cfam_1554, retro_cfam_1665, retro_cfam_1804, retro_cfam_1808, retro_cfam_2084, retro_cfam_2163, retro_cfam_241, retro_cfam_547, retro_cfam_762, retro_cfam_774, retro_cfam_806, retro_cfam_913,
Callithrix jacchus	ENSCJAG00000015601	10 retrocopies	retro_cjac_1424, retro_cjac_1647, retro_cjac_1946, retro_cjac_2077, retro_cjac_2084, retro_cjac_2366, retro_cjac_2861, retro_cjac_3259, retro_cjac_3271, retro_cjac_3308,
Cavia porcellus	ENSCPOG00000023542	1 retrocopy	retro_cpor_194,
Erinaceus europaeus	ENSEEUG00000004499	1 retrocopy	retro_eeur_179,
Echinops telfairi	ENSETEG00000017922	4 retrocopies	retro_etel_1747, retro_etel_1778, retro_etel_2148, retro_etel_222,
Gorilla gorilla	ENSGGOG00000022496	1 retrocopy	retro_ggor_2765,
Monodelphis domestica	ENSMODG00000019445	3 retrocopies	retro_mdom_1213, retro_mdom_1946, retro_mdom_431,
Mus musculus	ENSMUSG00000027479	2 retrocopies	retro_mmus_3160 , retro_mmus_3466,
Otolemur garnettii	ENSOGAG00000026557	2 retrocopies	retro_ogar_226, retro_ogar_2290,
Sorex araneus	ENSSARG00000002368	1 retrocopy	retro_sara_380,
Drosophila melanogaster	FBgn0027066	1 retrocopy	retro_dmel_83,