RetrogeneDB ID: retro_cfam_515

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:28601226..28602477(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDAD1
• Ensembl ID: ENSCAFG00000008521
• Aliases: None
• Description: SDA1 domain containing 1 [Source:HGNC Symbol;Acc:25537]

Sequence

>retro_cfam_515
GTGCTCAAGAAACAAAAAAAGAAGAAGAAACCAGAGGTGTTTAACTTTTCAGCTATTCATTTGATTCATGATCCCCAAGA
TTTTGCAGAAAAATTACTAAAACAACTAGAGAGCTCTACAAAGAGGTTTGAGGTGAAAATGATGCTCATGAACCTCATCT
CCAGATTGGTGGGAATTCATGAGCTTTTTCTCTTCAACTTCTATCCCTTTGTACAAAGATTTCTGCAACCTCACCAAAGA
GAAGTAACAAAGATCCTTCTGTTTCCTGCCCAAGCATCTCATCACTTAGTACCCCCAGAGATAATTCAGTCAGTGCTCAT
GACTGTGGCCAACAATTCTGTCACCAACAAGAACTCTGGGGAGGTCATGACAGTAGGAATCAATGCTATAAAAGAGATAA
CAGCTCGATATCCTCTAGCCATTACTGAAGAACTTCTCCAAGACCTAGCTCAGTATAAAACACACAGAGATAAGAATGTG
ATGATGTCTGCTAGAACTTTGATTCAGCTCTTCCGAACACTGAATCCTAAGATGTTGCAAAACTAATTCCGGGGTAAGCC
TACAGAGGCCTCCATAGAAGCAAGAGTGCAAGAATATGGAGAATTAGATGCTAAAGATTACATTCCAGAAGCATAAGTTC
TAGAAGTTGGAAAAGAAGAGAATACTGAAAATGTTGAAGATGGGTGGGAAAGTACCAGTCTCAGTGAGGAGGCAGATGCT
GATGGTGAGTGGGTTGATGTGCATCATTCTTCTGATGAAGAGTAGTAAGAAATATTCAAGAAGCTCAACAGGATGCCCAT
GGAGGAGCAGAAAGCCAAAGCTGCAGCCATTAGCACGAGCCAAGTTCTAACTTAAGAAGACTTCCAGAAAATCTGCATAG
CCCAAATGAGGAAAGAACTCGACACTACCCCAGGGAAAGCCCAAAAGAGAAAATACATTGAAATAGATAGTGATGAGGAG
CCTAGGGGTGAGTTACTTTCTCTTCGGGACATTGAACGCCTTCATAAAAAGCCAAAATCTGACAAGGAGACAAGATTAGC
AACAGCAGTGGCTGGAAAGACAGACCGAAAAGAATTTGTGAGGAAGAAAACCAAAATGAACCCATTTTCCAGTTCCACAA
ATAAAGGGAAGAAAAAACAGAAGAACTTTATGATGATGCGATATAGCCACAACGTTCGGTCAAAAGACAAGCGTTCCTTC
CGAGAAAAGCAGCTGGCACTACCAGATGCACTTTTGAAAAAGAGAAAAAAA

Alignment

ORF - retro_cfam_515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.82 %
• Parental protein coverage: 60.23 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFQKQKKKKKPEVFNFSAIHLIHDPQDFAEKLLKQLESSTERFEVKMMLMNLISRLVGIHELFLFNFYPF
          ...KQKKKKKPEVFNFSAIHLIHDPQDFAEKLLKQLESST.RFEVKMMLMNLISRLVGIHELFLFNFYPF
Retrocopy VLKKQKKKKKPEVFNFSAIHLIHDPQDFAEKLLKQLESSTKRFEVKMMLMNLISRLVGIHELFLFNFYPF

Parental  VQRFLQPHQREVTKILLFAAQASHHLVPPEIIQSVLMTVANNFVTDKNSGEVMTVGINAIKEITARCPLA
          VQRFLQPHQREVTKILLF.AQASHHLVPPEIIQSVLMTVANN.VT.KNSGEVMTVGINAIKEITAR.PLA
Retrocopy VQRFLQPHQREVTKILLFPAQASHHLVPPEIIQSVLMTVANNSVTNKNSGEVMTVGINAIKEITARYPLA

Parental  MTEELLQDLVQYKTHRDKNVMMSARTLIQLFRTLNPKMLQKKFRGKPTEASIEARVQEYGELDAKDYIPG
          .TEELLQDL.QYKTHRDKNVMMSARTLIQLFRTLNPKMLQ..FRGKPTEASIEARVQEYGELDAKDYIP.
Retrocopy ITEELLQDLAQYKTHRDKNVMMSARTLIQLFRTLNPKMLQN*FRGKPTEASIEARVQEYGELDAKDYIPE

Parental  AEVLEVGKEENAENVEGDGWESTSLSEEADADGEWIDVHHSSDEEQQEIFKKLNGMPMEERKAKAAAIST
          A.VLEVGKEEN.ENVE.DGWESTSLSEEADADGEW.DVHHSSDEE..EIFKKLN.MPMEE.KAKAAAIST
Retrocopy A*VLEVGKEENTENVE-DGWESTSLSEEADADGEWVDVHHSSDEE**EIFKKLNRMPMEEQKAKAAAIST

Parental  SRVLTQEDFQKIRIAQMRKELDATPGKAQKRKYIEIDNDEEPRGELLSLRDIERLHKKPKSDKETRLATA
          S.VLT.EDFQKI.IAQMRKELD.TPGKAQKRKYIEID.DEEPRGELLSLRDIERLHKKPKSDKETRLATA
Retrocopy SQVLT*EDFQKICIAQMRKELDTTPGKAQKRKYIEIDSDEEPRGELLSLRDIERLHKKPKSDKETRLATA

Parental  VAGKTDRKEFVRKKTKMNPFSSSTNKEKKKQKNFMMMRYSHNVRSKNKRSFREKQLALRDALLKKRKR
          VAGKTDRKEFVRKKTKMNPFSSSTNK.KKKQKNFMMMRYSHNVRSK.KRSFREKQLAL.DALLKKRK.
Retrocopy VAGKTDRKEFVRKKTKMNPFSSSTNKGKKKQKNFMMMRYSHNVRSKDKRSFREKQLALPDALLKKRKK

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	0.63 RPM	17.89 RPM
SRP017611_brain	0.48 RPM	18.58 RPM
SRP017611_kidney	0.66 RPM	14.59 RPM
SRP017611_liver	0.65 RPM	12.11 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_515 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_515 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_515 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008521	2 retrocopies	retro_cfam_1211, retro_cfam_515 ,
Echinops telfairi	ENSETEG00000004811	2 retrocopies	retro_etel_1946, retro_etel_779,
Gorilla gorilla	ENSGGOG00000006441	1 retrocopy	retro_ggor_1498,
Loxodonta africana	ENSLAFG00000012217	1 retrocopy	retro_lafr_980,
Microcebus murinus	ENSMICG00000006682	1 retrocopy	retro_mmur_1204,
Macaca mulatta	ENSMMUG00000017503	1 retrocopy	retro_mmul_604,
Nomascus leucogenys	ENSNLEG00000027034	1 retrocopy	retro_nleu_2410,
Rattus norvegicus	ENSRNOG00000022229	2 retrocopies	retro_rnor_1381, retro_rnor_1967,
Sus scrofa	ENSSSCG00000008974	1 retrocopy	retro_sscr_571,