RetrogeneDB ID: retro_mmus_3072

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:104501057..104502107(-)
• Located in intron of: ENSMUSG00000057596

Retrocopy information

• Ensembl ID: ENSMUSG00000082154
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ccnyl1
• Ensembl ID: ENSMUSG00000070871
• Aliases: Ccnyl1, 9630037P07Rik, AW554339
• Description: cyclin Y-like 1 [Source:MGI Symbol;Acc:MGI:2138614]

Sequence

>retro_mmus_3072
CCCAAGCTGGGCCGGCGCGCTGGGCCGGCAGAGCCCGACTACGAGTCCGAGGTCTAAGAGGCGGCGGCTGGGGACGCGGT
GGCGGTAGCGCCGGCGCCCGCTGCGGCCGTGGAGCCTGCCGAGTTGGATTTCGGAGCCGGGGAGGGCCACCACCTGCAGC
ACATCAGTGACCGAGAGATGCCCGAAGATCTAGCTTTGGAATCAAACCCTTCCGACCACCCGAGGGCAAGCACAATTTTC
CTGAGCAAATCTCAAACGGATGTGCGTGAAAAGAGGAAGAGCAACCATTTAAACCATGTATCTCCAGGGCAGCTTACTAA
AAAGTATAGCTCATGCTCAACAATATATCTAAATGACAGCACAGTCAGCCAGCCTAACCTTAGAACCACAATAAAATGTG
TGACCTTAGCAATATATTACCACATAAAGAACAGAGATGCAAATAGATCCCTGGACATTTTTGATGAGCGGTCACATCCT
CTCACAAGAGAGAAAGTTCCAGAGGAGTACTTTAAGCATGACCCTGAACACAAATTTATTTACAGATTTGTTCGTACACT
TTTTAGTGCTGCACAGCTGACAGCGGAATGTGCAATAGTGACGTTGGTTTACTTAGAGAGGCTCCTAACTTATGCTGAGA
TCGACATTTGTCCCACCAACTGGAAAAGAATTGTTCTGGGAGCCATTCTTCTTGCCTCCAAGGTTTGGGATGACCAGGCT
GTATGGAATGTAGACTACTGCCAGATCCTCAAGGACATTACGGTTGAGGACATGAATGAGATGGAAAGGCATTTCTTGGA
GCTACTCCAGTTTAATATTAATGTTCCTGCCAGTGTTTATGCCAAATACTACTTTGACCTTCGCTCCTTAGCAGATGACA
ACAACCTGAATTTTCTGTTTGCTCCTCTCAGCAAAGAAAGAGCACAGAACCTAGAGGCCATTTCAAGATTGTGTGAAGAC
AAATACAAAGACTTGTGTAGAGCTGCTATGAGAAGATCTTTAAGCGCTGATAATTTCATTGGTATTCAGCGCTCTAATGC
CATCCTCTCT

Alignment

ORF - retro_mmus_3072 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.14 %
• Parental protein coverage: 95.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKLGRRAGPAEPDYESEVYEAAAGDAVAVAPAPAAAVEPAELDFGAGEGHHLQHISDREMPEDLALESNP
          PKLGRRAGPAEPDYESEV.EAAAGDAVAVAPAPAAAVEPAELDFGAGEGHHLQHISDREMPEDLALESNP
Retrocopy PKLGRRAGPAEPDYESEV*EAAAGDAVAVAPAPAAAVEPAELDFGAGEGHHLQHISDREMPEDLALESNP

Parental  SDHPRASTIFLSKSQTDVREKRKSNHLNHVSPGQLTKKYSSCSTIFLDDSTVSQPNLRTTIKCVTLAIYY
          SDHPRASTIFLSKSQTDVREKRKSNHLNHVSPGQLTKKYSSCSTI.L.DSTVSQPNLRTTIKCVTLAIYY
Retrocopy SDHPRASTIFLSKSQTDVREKRKSNHLNHVSPGQLTKKYSSCSTIYLNDSTVSQPNLRTTIKCVTLAIYY

Parental  HIKNRDANRSLDIFDERSHPLTREKVPEEYFKHDPEHKFIYRFVRTLFSAAQLTAECAIVTLVYLERLLT
          HIKNRDANRSLDIFDERSHPLTREKVPEEYFKHDPEHKFIYRFVRTLFSAAQLTAECAIVTLVYLERLLT
Retrocopy HIKNRDANRSLDIFDERSHPLTREKVPEEYFKHDPEHKFIYRFVRTLFSAAQLTAECAIVTLVYLERLLT

Parental  YAEIDICPTNWKRIVLGAILLASKVWDDQAVWNVDYCQILKDITVEDMNEMERHFLELLQFNINVPASVY
          YAEIDICPTNWKRIVLGAILLASKVWDDQAVWNVDYCQILKDITVEDMNEMERHFLELLQFNINVPASVY
Retrocopy YAEIDICPTNWKRIVLGAILLASKVWDDQAVWNVDYCQILKDITVEDMNEMERHFLELLQFNINVPASVY

Parental  AKYYFDLRSLADDNNLNFLFAPLSKERAQNLEAISRLCEDKYKDLCRAAMRRSLSADNFIGIQRSNAILS
          AKYYFDLRSLADDNNLNFLFAPLSKERAQNLEAISRLCEDKYKDLCRAAMRRSLSADNFIGIQRSNAILS
Retrocopy AKYYFDLRSLADDNNLNFLFAPLSKERAQNLEAISRLCEDKYKDLCRAAMRRSLSADNFIGIQRSNAILS

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	9.70 RPM
SRP007412_cerebellum	0.00 RPM	4.39 RPM
SRP007412_heart	0.00 RPM	6.13 RPM
SRP007412_kidney	0.00 RPM	6.03 RPM
SRP007412_liver	0.05 RPM	2.59 RPM
SRP007412_testis	0.18 RPM	55.89 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3072 was not detected

EST

No EST(s) were mapped for retro_mmus_3072 retrocopy.

TSS

No TSS is located nearby retro_mmus_3072 retrocopy 5' end.

Lab

retro_mmus_3072 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3072 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001008	1 retrocopy	retro_cjac_3555,
Callithrix jacchus	ENSCJAG00000002901	1 retrocopy	retro_cjac_569,
Callithrix jacchus	ENSCJAG00000011445	1 retrocopy	retro_cjac_1164,
Callithrix jacchus	ENSCJAG00000034702	1 retrocopy	retro_cjac_610,
Gorilla gorilla	ENSGGOG00000008136	1 retrocopy	retro_ggor_1229,
Macaca mulatta	ENSMMUG00000020211	1 retrocopy	retro_mmul_2587,
Mus musculus	ENSMUSG00000070871	1 retrocopy	retro_mmus_3072 ,
Nomascus leucogenys	ENSNLEG00000007131	3 retrocopies	retro_nleu_1164, retro_nleu_2902, retro_nleu_430,
Pongo abelii	ENSPPYG00000013118	3 retrocopies	retro_pabe_1345, retro_pabe_3766, retro_pabe_76,
Pan troglodytes	ENSPTRG00000008072	1 retrocopy	retro_ptro_1091,