RetrogeneDB ID: retro_cfam_925

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:22348551..22349984(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MICU1
• Ensembl ID: ENSCAFG00000014489
• Aliases: None
• Description: mitochondrial calcium uptake 1 [Source:HGNC Symbol;Acc:1530]

Sequence

>retro_cfam_925
ATGTTTCCTCTTAACTCCCTTTCTGCATTGGCAGAACTGGCTGTGGGCTCTCGATGTTACCATAGAGGATCATAGCCCAC
CCAGATCAGGTGACAACTAATGATGGTGGCTTTCCTAGGAGCATCTGCAGTAACTGCAAGTACAGGTCTCCTGTGGAAGA
GGGCCCTTGCAGAATCTCCACCATCTGTAAACAACCTAAAGAATGAACTTGGTGATAAAAGGAAGAATAAAGATGAAGGG
GAGGTTTGTAACCATGAAAAAAGGCTGCAGGTGTTTGTCTTGAGCCTCATCAGGAAGAGAAAAAGAAGAAACATTTTGGA
TTCAGAGACAGAAAAGTGATGGAATATGAGAATAGGATTCGAGTGTATTCCACACCAGACAAAATCATCCAATATTTTGC
CACCTTGAAAGTAATCAATGAACCTGGTGAATCTGAAGTGTTTATGACTCCACAAGATTTTGTGTGATTCATAACACGCA
ATGAAAAACAACCAGAAAACTTGGGTCTAGATCAATATACAATAAAATGCTTTGATGGAAAGAAAACTGCCCAGGAACGA
GAAAAATTTGCTGATGAAGGCAGTATATTCTATACCCTTGGAGAATGTGGACTCATATCCTTTTTGGACTACATTTTCCT
TACAACTGTTCTTTCTACTCCTCAGAAAAATTTTGAAGTTGCCTTCAAGATGTTTGACTTGACTGGATATGGAGAAGTAG
ACATGGAGGAGTTTGAGTAGGTTCAGAGCATCATTTGCTCCCAAACCAGTACGGGTATGTGTCACAGAGATCGTCCTACT
ACTGGTAACACTCTAAAGTCTGGCTTGTGTTCAGCCCTCACAACCTACTCCTTTGGAGCTGATCTTAAGGGGTAGCTGAC
AATCAAAAACTTCCTTGAATTTCAGGGTAAACTTCAGCATGATGTTCTGAAATTAGGGTTCGAACACCATGATCCTGTGG
ATAGGAAAATTACTGAGAGGCAGTTCAGTGGCATGCTGCTGGCCTACAGTGGACTGCAGTCTAAGAAGTTGACTGCCATG
CAGAAGCAGCTCAAGAAGCACTTCAAAGAGGGAAAGGGTCTGACATTTCAGGAAGTGGATGACTTCTTTACTTTCCTAAA
GAATATTAATGATGTGGACACTGCATTCAGCTTTTAGCATATGGCAGGGCCATCTCTTGGTAAAGTGACCATGCAGCAGG
TGGCCAGGACAACAGCTAAAGTGGAACTCTCCAACCATGTGTGTGATGTGGTGTTTGTGCTCTTTGACTGCGATGGCAAT
GGGGAGCTGAGCAATAAGGAATTTGTTTCCATCATGAAGCAGCGGCTGATGAGAGGCCTAGAGAAGCCCAAAGTCATGGG
CTTCACCCGCCTCATGCAGGCCATGTGGAAGTGCACACAGAAAACTGCCTGGGACTTCGCTTTGCCTAAACAG

Alignment

ORF - retro_cfam_925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFRLNSLSALAELAVGSRCYHGGSQPTQIRRRLMMVAFLGASAVTASTGLLWKRALAESPPSVNNLKNEL
          MF.LNSLSALAELAVGSRCYH.GS.PTQIR..LMMVAFLGASAVTASTGLLWKRALAESPPSVNNLKNEL
Retrocopy MFPLNSLSALAELAVGSRCYHRGS*PTQIR*QLMMVAFLGASAVTASTGLLWKRALAESPPSVNNLKNEL

Parental  GDKGKNKDEGEVCNHEK-KAAGVCLEPHQEEKKKKRSGFRDRKVMEYENRIRAYSTPDKIFRYFATLKVI
          GDK.KNKDEGEVCNHEK.KAAGVCLEPHQEEKKKK..GFRDRKVMEYENRIR.YSTPDKI..YFATLKVI
Retrocopy GDKRKNKDEGEVCNHEK<KAAGVCLEPHQEEKKKKHFGFRDRKVMEYENRIRVYSTPDKIIQYFATLKVI

Parental  NEPGESEVFMTPQDFVRSITPNEKQPENLGLDQYTIKRFDGKKIAQEREKFADEGSIFYTLGECGLISFS
          NEPGESEVFMTPQDFV..IT.NEKQPENLGLDQYTIK.FDGKK.AQEREKFADEGSIFYTLGECGLISF.
Retrocopy NEPGESEVFMTPQDFV*FITRNEKQPENLGLDQYTIKCFDGKKTAQEREKFADEGSIFYTLGECGLISFL

Parental  DYIFLTTVLSTPQRNFEIAFKMFDLNGDGEVDMEEFEQVQSIIRSQTSMGMRHRDRPTTGNTLKSGLCSA
          DYIFLTTVLSTPQ.NFE.AFKMFDL.G.GEVDMEEFE.VQSII.SQTS.GM.HRDRPTTGNTLKSGLCSA
Retrocopy DYIFLTTVLSTPQKNFEVAFKMFDLTGYGEVDMEEFE*VQSIICSQTSTGMCHRDRPTTGNTLKSGLCSA

Parental  LTTYFFGADLKGKLTIKNFLEFQRKLQHDVLKLEFERHDPVDGKITERQFGGMLLAYSGVQSKKLTAMQK
          LTTY.FGADLKG.LTIKNFLEFQ.KLQHDVLKL.FE.HDPVD.KITERQF.GMLLAYSG.QSKKLTAMQK
Retrocopy LTTYSFGADLKG*LTIKNFLEFQGKLQHDVLKLGFEHHDPVDRKITERQFSGMLLAYSGLQSKKLTAMQK

Parental  QLKKHFKEGKGLTFQEVENFFTFLKNINDVDTALSFYHMAGASLDKVTMQQVARTVAKVELSDHVCDVVF
          QLKKHFKEGKGLTFQEV..FFTFLKNINDVDTA.SF.HMAG.SL.KVTMQQVART.AKVELS.HVCDVVF
Retrocopy QLKKHFKEGKGLTFQEVDDFFTFLKNINDVDTAFSF*HMAGPSLGKVTMQQVARTTAKVELSNHVCDVVF

Parental  ALFDCDGNGELSNKEFVSIMKQRLMRGLEKPKDMGFTRLMQAMWKCAQETAWDFALPKQ
          .LFDCDGNGELSNKEFVSIMKQRLMRGLEKPK.MGFTRLMQAMWKC.Q.TAWDFALPKQ
Retrocopy VLFDCDGNGELSNKEFVSIMKQRLMRGLEKPKVMGFTRLMQAMWKCTQKTAWDFALPKQ

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
SRP012049_cerebellum	0.00 RPM	46.74 RPM
SRP017611_brain	0.16 RPM	36.92 RPM
SRP017611_kidney	0.13 RPM	95.62 RPM
SRP017611_liver	0.00 RPM	25.16 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_925 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_925 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014489	1 retrocopy	retro_cfam_925 ,