RetrogeneDB ID: retro_mmus_1170

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:8409369..8410193(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccnb1
• Ensembl ID: ENSMUSG00000041431
• Aliases: Ccnb1, Ccnb1-rs1, Ccnb1-rs13, CycB1, Cycb-4, Cycb-5, Cycb1-rs1
• Description: cyclin B1 [Source:MGI Symbol;Acc:MGI:88302]

Sequence

>retro_mmus_1170
GCAGATGATGGAGCTGACCCAAACCTCTGTAGTGAATATGTGAAAGATATCTATGCTTATCTCCGACAACTGGAGGAAGA
GCAGTCAGTTAGACCAAAATACCTACAGGGTCGTGAAGTGACTGGAAACATGAGAGCTATCCTCATTGACTGGCTAATAC
AGGTTCAGATGAAATTTAGGCTGCTTCAGGAGACCATGTTTATGACTGTGTCCATGATTGATCGGTTCATGCAGAACAGT
TGTGTGCCCAAGAAGGTGCTGCAGCTGGTCGGTGTAACTGCCATGTTTATCGCAAGCAAATATGAGATGTACCCTCCAGA
AATAGGTGACTTCGCCTTTGTGACTAACAACACCTAGCTAAGCACCAGATCAGACAGATGGAGATGAAGATTCTCAGAGT
TCTGAACTTCAGCCTGGGTCACCCTCTGCCTCTGCACTTCCTCCGCAGAGCATCTAAAGTCGGAGAGGTTGACGTCGAGC
AGCACACTTTGGCCAAATACCTCATGGAGCTCTCCATGCTGGACTACGACATGGTGCATTTTGCTCCTTCTCAAATTGCA
GCTGGGGCTTTCTGCTTAGCGCTGAAAATTCTTGACAACGGTGAATGGACACCAACTCTGCAGCACTACCTATCCTACAC
GGAAGACTCCCTGCTTCCTGTTATGTAGCACCTGGCTAAGAATGTAGTCATGGTGAACTGTGGCCTTACAAAGCACATGA
CTGTCAAGAACAAGTATGCAGCATCTAAGCATGCTAAGATCAGCACGCTGGCACGGCTGAACTGTACACTAGTTCAGAAT
TTGTCTAAGGCCGTGACAAAGGCA

Alignment

ORF - retro_mmus_1170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.03 %
• Parental protein coverage: 64.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ADDGADPNLCSEYVKDIYAYLRQLEEEQSVRPKYLQGREVTGNMRAILIDWLIQVQMKFRLLQETMYMTV
          ADDGADPNLCSEYVKDIYAYLRQLEEEQSVRPKYLQGREVTGNMRAILIDWLIQVQMKFRLLQETM.MTV
Retrocopy ADDGADPNLCSEYVKDIYAYLRQLEEEQSVRPKYLQGREVTGNMRAILIDWLIQVQMKFRLLQETMFMTV

Parental  SIIDRFMQNSCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTNNT-YTKHQIRQMEMKILRVLNFS
          S.IDRFMQNSCVPKK.LQLVGVTAMFIASKYE.MYPPEIGDFAFVTNNT...KHQIRQMEMKILRVLNFS
Retrocopy SMIDRFMQNSCVPKKVLQLVGVTAMFIASKYE-MYPPEIGDFAFVTNNT<LAKHQIRQMEMKILRVLNFS

Parental  LGRPLPLHFLRRASKVGEVDVEQHTLAKYLMELSMLDYDMVHFAPSQIAAGAFCLALKILDNGEWTPTLQ
          LG.PLPLHFLRRASKVGEVDVEQHTLAKYLMELSMLDYDMVHFAPSQIAAGAFCLALKILDNGEWTPTLQ
Retrocopy LGHPLPLHFLRRASKVGEVDVEQHTLAKYLMELSMLDYDMVHFAPSQIAAGAFCLALKILDNGEWTPTLQ

Parental  HYLSYSEDSLLPVMQHLAKNVVMVNCGLTKHMTVKNKYAASKHAKISTLAQLNCTLVQNLSKAVTKA
          HYLSY.EDSLLPVM.HLAKNVVMVNCGLTKHMTVKNKYAASKHAKISTLA.LNCTLVQNLSKAVTKA
Retrocopy HYLSYTEDSLLPVM*HLAKNVVMVNCGLTKHMTVKNKYAASKHAKISTLARLNCTLVQNLSKAVTKA

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	0.56 RPM
SRP007412_cerebellum	0.00 RPM	0.09 RPM
SRP007412_heart	0.00 RPM	0.28 RPM
SRP007412_kidney	0.00 RPM	0.40 RPM
SRP007412_liver	0.00 RPM	0.11 RPM
SRP007412_testis	0.32 RPM	28.54 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1170 was not detected

EST

No EST(s) were mapped for retro_mmus_1170 retrocopy.

TSS

No TSS is located nearby retro_mmus_1170 retrocopy 5' end.

Lab

retro_mmus_1170 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1170 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007705	1 retrocopy	retro_cfam_213,
Callithrix jacchus	ENSCJAG00000016075	1 retrocopy	retro_cjac_4137,
Cavia porcellus	ENSCPOG00000014629	1 retrocopy	retro_cpor_13,
Felis catus	ENSFCAG00000001572	1 retrocopy	retro_fcat_840,
Mustela putorius furo	ENSMPUG00000014648	1 retrocopy	retro_mputfur_58,
Mus musculus	ENSMUSG00000034165	1 retrocopy	retro_mmus_2519,
Mus musculus	ENSMUSG00000041431	5 retrocopies	retro_mmus_1170 , retro_mmus_1550, retro_mmus_2508, retro_mmus_2615, retro_mmus_3023,
Procavia capensis	ENSPCAG00000002451	1 retrocopy	retro_pcap_176,
Rattus norvegicus	ENSRNOG00000018635	2 retrocopies	retro_rnor_568, retro_rnor_814,
Sarcophilus harrisii	ENSSHAG00000007685	1 retrocopy	retro_shar_290,
Tupaia belangeri	ENSTBEG00000011817	4 retrocopies	retro_tbel_1185, retro_tbel_3200, retro_tbel_4185, retro_tbel_4531,