RetrogeneDB ID: retro_mmus_3165

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:124765260..124766214(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gtf2b
• Ensembl ID: ENSMUSG00000028271
• Aliases: None
• Description: general transcription factor IIB [Source:MGI Symbol;Acc:MGI:2385191]

Sequence

>retro_mmus_3165
GCGTCGACCAGCCGTTTGGATGCTCTCCCAACAGCCACGTGTCCAAATCATCCAGATGCAAATTTAGTCGAGGACTACAG
AGCTGGCGATGTGATCTGTCCCGAATGGGGCCTAGTTGTAGGGGACCGAGTTATTGATGTGGGATCTGAATGGAGAACTT
TCAGAATGACAACGTCGAATGACAACGCAACAAAAGACCCATTTCGAGTTGGAGACTCTCAGAATCCTCTTCTGAGTGAT
GAAGATTTGTCCACCACGATTGGCAAGGGTACAGGAGCTGTAAGCTTTGAGAGTTGGGCAATTCTAAGTATCCGAACCAG
AGAACAATGAGTAGTTCTGATAGAGCGTTGATGAACGCATTCAAGGAAATCACGACCATGGCGGACAGAATCAACCTCCT
CGCAATATAGTTAATCGAACGGATAATTTATTCAAGCAAGTGTATGAGCAGAAGAGCCTGAAGGGAAGAGCTAATGACGC
GATAGCTTCTGCTTGTCTGTACAGCGCCTGTAGACAAGAAGGCGTTCCCAGGACCTTTAAGAAATAATGTGCTATGTCTT
GAATCTCCAAGAAAGAAATTGGCCACTGTTTTAAACAGATTTTGAAAGCTCTGGAAACCAGCGTAGATCTGACCACAGCT
GGGGACTTCATGTCCAGGTTCTGCTCCAATCTTTGCCTCCCCAAGCAAGTGCAGAGGGCAGCTACACACATAGCCCGCAA
GGCTGTGGAGCTGGACTTGGTTCCTGGCAGGAGCCCGATCTCTGTGGCCGCGGCGGCAGCTATTTACATGGCTTCCCAGG
CTTCAGCTGAGAAGCGAACACAGAAGTCGTGGATATTGCTGGTGTTGCTGATGTTACAATCCGACCATCCTACAGACTGA
TTTACCCTCGGGCTCCAGATCTCTTCCCATCAGACTTAAAGTGTGACACCCCAGTGGACAAATTACCCCAGCTT

Alignment

ORF - retro_mmus_3165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.23 %
• Parental protein coverage: 99.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASTSRLDALPRVTCPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTF----SNDKATKDPSRV
          ASTSRLDALP..TCPNHPDA.LVEDYRAGD.ICPE.GLVVGDRVIDVGSEWRTF....SND.ATKDP.RV
Retrocopy ASTSRLDALPTATCPNHPDANLVEDYRAGDVICPEWGLVVGDRVIDVGSEWRTFRMTTSNDNATKDPFRV

Parental  GDSQNPLLSDGDLSTMIGKGTGAASFD-EFGNSKYQNRRTMSSSDRAMMNAFKEITTMADRINL-PRNIV
          GDSQNPLLSD.DLST.IGKGTGA.SF..E.GNSKY.N.RTMSSSDRA.MNAFKEITTMADRINL.PRNIV
Retrocopy GDSQNPLLSDEDLSTTIGKGTGAVSFE<ELGNSKYPNQRTMSSSDRALMNAFKEITTMADRINL<PRNIV

Parental  DRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKLILKALETS
          .RT.NLFKQVYEQKSLKGRANDAIASACLY.ACRQEGVPRTFK..CA.S.ISKKEIG.CFK.ILKALETS
Retrocopy NRTDNLFKQVYEQKSLKGRANDAIASACLYSACRQEGVPRTFKK*CAMS*ISKKEIGHCFKQILKALETS

Parental  VDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQK-EI
          VDL.T.GDFMSRFCSNLCLPKQVQ.AATHIARKAVELDLVPGRSPISVAAAA................E.
Retrocopy VDLTTAGDFMSRFCSNLCLPKQVQRAATHIARKAVELDLVPGRSPISVAAAAAIYMASQASAEKRTQ<EV

Parental  GDIAGVADVTIRQSYRLIYPRAPDLFPSDFKFDTPVDKLPQL
          .DIAGVADVTIR.SYRLIYPRAPDLFPSD.K.DTPVDKLPQL
Retrocopy VDIAGVADVTIRPSYRLIYPRAPDLFPSDLKCDTPVDKLPQL

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	20.28 RPM
SRP007412_cerebellum	0.00 RPM	20.19 RPM
SRP007412_heart	0.00 RPM	12.30 RPM
SRP007412_kidney	0.06 RPM	20.58 RPM
SRP007412_liver	0.00 RPM	15.40 RPM
SRP007412_testis	1.01 RPM	51.41 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3165 was not detected

EST

No EST(s) were mapped for retro_mmus_3165 retrocopy.

TSS

No TSS is located nearby retro_mmus_3165 retrocopy 5' end.

Lab

retro_mmus_3165 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3165 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000028271	1 retrocopy	retro_mmus_3165 ,
Sarcophilus harrisii	ENSSHAG00000005314	1 retrocopy	retro_shar_585,
Tupaia belangeri	ENSTBEG00000001398	2 retrocopies	retro_tbel_1988, retro_tbel_2988,
Tursiops truncatus	ENSTTRG00000011903	1 retrocopy	retro_ttru_1823,