RetrogeneDB ID: retro_mmus_1640

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:45163229..45164168(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccdc94
• Ensembl ID: ENSMUSG00000003208
• Aliases: Ccdc94, 2900016D05Rik, AI413813
• Description: coiled-coil domain containing 94 [Source:MGI Symbol;Acc:MGI:1920136]

Sequence

>retro_mmus_1640
ATGTCCGAACGGAAAGTTTTAAACAAATACTACCCACCTGACTTTGACCCATCGAAGATCCCGAAACTCAAGCTACCCAA
GGACCGGCAGTATGTGGTGCGGCTGATGGCCCCCTTCAACATGAGGTGTAAGACTTGTGGAGAGTACATCTACAAAGGGA
AGAAGTTCAACGCACGAAAGGAAACAGTCCAGAATGAGGCCTACCTGGGCCTGTCAATCTTCCGATTCTACATCAAGTGC
ACGCGCTGCTTGGCTGAGATCACCTTCAAGACGGACCCAGAGAACACGGACTACACCATGGAGCACGGGGCCACGCGCAA
CTTCCAGGCGGAGAAGCTTTTGGAGGAGGAGGAGAAGCGCGTGCAGAAGGAGCGAGAGGACGAGGAACTGAACAACCCCA
TGAAGGTCCTAGAGAACCGGACAAAGGACTCCAAGCTGGAGATGGAAGTGCTGGCAAACCTGCAAGAGCTGAAAGACCTC
AACCAGCGGCAGGCACACGTGGATTTCGAGGCCATGCTGCGGCAACACCGCCTGTCTCAGGAGCAGTGGCGACAGCAGCA
GGAGGAGGAAGATGAGCTGGAGACAGCTGCCTTGCTGCAGGAGGCTCACCATCGAAGGCTTCCGGATGACTCCGACTCAG
AGGATGAGGCTCCACCTTCCCGACTACAGGCAGCTGCAAGACCCAACCCCACGACCAGCCTCCACAAGGTACCAAAGACC
AAGAGGAAGGCAGAGGCCCTGTGCGGCAAAGCACAGTTGGCAGGCTTGGTTGTACCAAAGAAGGTAAAGACGGAAGCCAA
AGGGGGCTCAGAGCAAGTCAAGGTGTCCACCGCAGGTGCCCCCGAGAACAGGAAGACAGCCAACCCTACACCCCAGACAT
CTGCTGCGTCCTCCCTGAGCCAGCTGGGTGCATACAGGGATAACAAGGACAGTGACAAC

Alignment

ORF - retro_mmus_1640 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSERKVLNKYYPPDFDPSKIPKLKLPKDRQYVVRLMAPFNMRCKTCGEYIYKGKKFNARKETVQNEAYLG
          MSERKVLNKYYPPDFDPSKIPKLKLPKDRQYVVRLMAPFNMRCKTCGEYIYKGKKFNARKETVQNEAYLG
Retrocopy MSERKVLNKYYPPDFDPSKIPKLKLPKDRQYVVRLMAPFNMRCKTCGEYIYKGKKFNARKETVQNEAYLG

Parental  LPIFRFYIKCTRCLAEITFKTDPENTDYTMEHGATRNFQAEKLLEEEEKRVQKEREDEELNNPMKVLENR
          L.IFRFYIKCTRCLAEITFKTDPENTDYTMEHGATRNFQAEKLLEEEEKRVQKEREDEELNNPMKVLENR
Retrocopy LSIFRFYIKCTRCLAEITFKTDPENTDYTMEHGATRNFQAEKLLEEEEKRVQKEREDEELNNPMKVLENR

Parental  TKDSKLEMEVLENLQELKDLNQRQAHVDFEAMLRQHRMSQEQWQQQQEEEDERETAALLEEARHRRLLED
          TKDSKLEMEVL.NLQELKDLNQRQAHVDFEAMLRQHR.SQEQW.QQQEEEDE.ETAALL.EA.HRRL..D
Retrocopy TKDSKLEMEVLANLQELKDLNQRQAHVDFEAMLRQHRLSQEQWRQQQEEEDELETAALLQEAHHRRLPDD

Parental  SESEDEAPPSRPRAAARPNPTAILNEVPQTKRKAEALCSKAQLAGLVVPKKVKTEANGASEQVGVPTAAG
          S.SEDEAPPSR..AAARPNPT..L..VP.TKRKAEALC.KAQLAGLVVPKKVKTEA.G.SEQV.V.T.AG
Retrocopy SDSEDEAPPSRLQAAARPNPTTSLHKVPKTKRKAEALCGKAQLAGLVVPKKVKTEAKGGSEQVKVST-AG

Parental  APKSRKADNPTPQTPGTSSLSQLGAYGDSEDSDS
          AP..RK..NPTPQT...SSLSQLGAY.D..DSD.
Retrocopy APENRKTANPTPQTSAASSLSQLGAYRDNKDSDN

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	0.05 RPM	4.63 RPM
SRP007412_cerebellum	0.00 RPM	8.12 RPM
SRP007412_heart	0.00 RPM	5.17 RPM
SRP007412_kidney	0.02 RPM	5.31 RPM
SRP007412_liver	0.00 RPM	2.79 RPM
SRP007412_testis	0.05 RPM	6.13 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1640 was not detected

EST

No EST(s) were mapped for retro_mmus_1640 retrocopy.

TSS

No TSS is located nearby retro_mmus_1640 retrocopy 5' end.

Lab

retro_mmus_1640 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1640 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000022785	1 retrocopy	retro_ecab_347,
Monodelphis domestica	ENSMODG00000000841	1 retrocopy	retro_mdom_496,
Mus musculus	ENSMUSG00000003208	1 retrocopy	retro_mmus_1640 ,
Otolemur garnettii	ENSOGAG00000001662	1 retrocopy	retro_ogar_168,
Sarcophilus harrisii	ENSSHAG00000010428	1 retrocopy	retro_shar_394,