RetrogeneDB ID: retro_mmus_1690

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:9538749..9539560(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Angel2
• Ensembl ID: ENSMUSG00000026634
• Aliases: Angel2, 2610307I21Rik, 5730410O10Rik, AI845692, D1Ertd396e, D1Ertd654e
• Description: angel homolog 2 (Drosophila) [Source:MGI Symbol;Acc:MGI:1196310]

Sequence

>retro_mmus_1690
TTGTTACACTGGAGTTTTCGCTTCCCCAATATTTTGAAAGAAATCATACATTTTGATGCAGATGTGCTTTGTCTGCTGAA
AGTTCAAGATCATTATGGGACAGAGATCAGGCCAAGTCTAGAATCACTGGGTTATCACTGTGAATATAAGATGAAAACAG
GAAGGAAGCCGGATGGCTGTGCCACCTGCCTCAAACATTCCAAGTTCTCCCTCTTATCTGTGAACCCAGTAGAGTTCTGC
CACTGTAATATTCCTCTGCTGGACAGAGAACAACATTGGATTAGTTTTACTCCTGCATCCCAAGGTCCCACATGCTGCCT
CTCCATCTGTCTGGATAGCTAACACACATCTGCTGTATAATCCTCGGTGTGGTGATATTAAGCTGACCCACCTGGTGATG
CTGCTAGCAGAGATTGCCAATGTGACCCATTACAAAGATGGCAGCTCCTGTCCCATTGTCATGTGTGGTGACTTTAATTC
TGTTCCTGGTTCTCCACTCTATAGCTTCATAAAGGAAGGGAAATTAAATTACGAAGGTCTTGCAATTGGAAAGGTATCTG
ACCAGGAACAGTCTTCACAGGGACAAAGAATTTTATCTATTCCAATTTGGCCCTCAAACCTAGGCATCTCTCAGAACTCT
GTTTATGAGGCACAACAGGTTCCCAAAGTAGAAAAGACAGTGATCTGACTCAAGCACAGCAGTAGAAAGGGGAGGTCCCA
GTGTCAACTGACAAAGTCGCATCTACAGCACAGTTTCAGCTTGTCATCTGTCTATTCCCATTATGCTCCTGACACCGAAG
TTCCCGAAGTG

Alignment

ORF - retro_mmus_1690 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 52.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLHWSFRFPNILKEIKHFDADVLCLQEVQEDHYGTEIRPSLESLGYHCEYKMKTGRKPDGCAICFKHSRF
          .LHWSFRFPNILKEI.HFDADVLCL..VQ.DHYGTEIRPSLESLGYHCEYKMKTGRKPDGCA.C.KHS.F
Retrocopy LLHWSFRFPNILKEIIHFDADVLCLLKVQ-DHYGTEIRPSLESLGYHCEYKMKTGRKPDGCATCLKHSKF

Parental  SLLSVNPVEFCRRDIPLLDRD-NIGLVLLLQPKIPRAASPSICIANTHLLYNPRRGDIKLTQLAMLLAEI
          SLLSVNPVEFC...IPLLDR..NIGLVLLL.PK.P.AASPS..IANTHLLYNPR.GDIKLT.L.MLLAEI
Retrocopy SLLSVNPVEFCHCNIPLLDRE>NIGLVLLLHPKVPHAASPSVWIANTHLLYNPRCGDIKLTHLVMLLAEI

Parental  ANVTHRKDGSSCPIVMCGDFNSVPGSPLYSFIKEGKLNYEGLAIGKVSGQEQSSRGQRILSIPIWPPNLG
          ANVTH.KDGSSCPIVMCGDFNSVPGSPLYSFIKEGKLNYEGLAIGKVS.QEQSS.GQRILSIPIWP.NLG
Retrocopy ANVTHYKDGSSCPIVMCGDFNSVPGSPLYSFIKEGKLNYEGLAIGKVSDQEQSSQGQRILSIPIWPSNLG

Parental  ISQNCVYEAQQVPKVEKTDSDVTQAQQEKAEVPVSADKVSSHLQHGFSLSSVYSHYVPDTGVPEV
          ISQN.VYEAQQ...V.K....V..................SHLQH.FSLSSVYSHY.PDT.VPEV
Retrocopy ISQNSVYEAQQ---VPKVEKTVI*LKHSSRKGRSQCQLTKSHLQHSFSLSSVYSHYAPDTEVPEV

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	0.02 RPM	51.02 RPM
SRP007412_cerebellum	0.00 RPM	48.07 RPM
SRP007412_heart	0.00 RPM	24.34 RPM
SRP007412_kidney	0.02 RPM	43.45 RPM
SRP007412_liver	0.03 RPM	26.54 RPM
SRP007412_testis	0.55 RPM	40.02 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1690 was not detected

EST

No EST(s) were mapped for retro_mmus_1690 retrocopy.

TSS

No TSS is located nearby retro_mmus_1690 retrocopy 5' end.

Lab

retro_mmus_1690 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1690 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003875	1 retrocopy	retro_cpor_1547,
Mus musculus	ENSMUSG00000026634	1 retrocopy	retro_mmus_1690 ,