RetrogeneDB ID: retro_cfam_1930

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:2420716..2422408(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000011085
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BARD1
• Ensembl ID: ENSCAFG00000014264
• Aliases: None
• Description: BRCA1 associated RING domain 1 [Source:HGNC Symbol;Acc:952]

Sequence

>retro_cfam_1930
GAAATCAACCAAAAATGGAATTTAGAAGCAGAAAAAGAAGATGATGAACTTGACTCCAAAGAGGAATTTAAGGAGAAGCT
GGTGTCTTTCTGTAGCCAGCCCTCTGTTAACCCTAATCCTCAGGCAAATGGTGAAATAGACTTACTTGCAAGTGGCTCTG
TAACAGAGTCACAGTGTTTTAGCAGCTTAGCTGAAGTCTCTTTACCATTAGCTGAGCAAATAGAGTCTCCAGAATTGGAG
AGCAGGAATGAAGAATTGACTCCCCAGAAGAATCTCTGTGAGAATCCTCTTCCACCTAAGCAGTCTTTGCCATCAGGTCA
CAGTGGGCACCGTGGGCAGCACAGCAGCCGGTCCAGTCCCATTTCTAAGAGATGCAGAAGCAGCATTCCTGGCACCAGTA
GCCAGCACATAGTGCTTTCAGAAAACAAGCCATTGCCTGGCTGCTCTTCACCACCTTCAAGCAAACTTAAAATTGGTGAC
ACATTAAGGAGGAAAAACAGTAATCTATCAGTTGAGTCCATGACCCTTTCACCAGGTACACCGCCTTCTGCCCTGAATAA
CCCAAGTTACAGACGGATGATGTCTAGCCCCTCAGCAACAAAGCTGTCACCCAATAGCCTTACAGCCGTGAAGAGAAATC
ATAGAGGAGAGACTCTGCTCCATATTGCTTCAATTAAGGGTGATGTACCTTCTGTTGAGTACCTCTTACAAAATGGAAGC
GACCCAAATGTTAAAGACCATGCTGGATGGACACCATTGCATGAAGCCTGCAATCATAGGCACCTGAAGGTAGTGGAGTT
GTTGGTGCAGCACCAGGCGTTGGTGAACACTCCTGGCTATCAGAACGACTCCCCGCTTCACAATGCTGCCAGGAACGGGC
ACTTGGAGATAGTCAAGCTCTTACTCGCCTCTGGAGCCTCCAGGGATGCCATTAACATATTTGGTTTGCGGCCTGTGGAT
TATGCAGACAATGAAAATATGAAATCACTATTGCTGCTACCAGAGAAGAATGAATCATCATCAACTCGCCATTACTCAGT
ACCAAACACTGGTCAGCGTAGGGATGGACCTCTTGTGCTTATAGGCAGTGGGCTTTCTTCAGAACAGAAAATGCTCAGTG
AGCTTGCAGCAATTCTTAAGGCTAAAAAATGTGCTGAATTTGACAATACAGTAACTCATGTCATTGTTCCTGGGGATACA
GTTCAAAGTACCCTGAAATGTATGCTTGGGATTCTCAATGGATGTTGGATCTTAAAATTTGAATGGGTGAAAGCATGTCT
ACAGAGAAAAGCATGTGAACAAGAGGAAAAATATGAGATACCTGAGGGACCCCATCGAAGCAGGCTCAACAAGGAACAGC
TGCTGCCAAAGCTGTTTGACGGATGCTACTTCTATTTTGGGGGAACCTTCAAACACCATCCCAAGGACAACCTTATTAAG
CTTGTCACTGCTGCTGGGGGCCAGGTCCTCAGTCGAAAGCCCAAGCCAGACAGTGATGTGACTCAGACCATCAATACGGT
TGCGTACCACGCGAGACCAGATTCCGATCAGCGCTTCTGCACACAGTATATCATCTACGAAGATTTGTCTAATCATCACC
CAAAGAGGGTTCGGCAGGGCAAAGTCTGGATGGCTCCTTCCAGCTGGTTTATAGATTGTGTGATGTCCTTTGAGTTGCTC
CCTCTTGACAGC

Alignment

ORF - retro_cfam_1930 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.88 %
• Parental protein coverage: 77.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EINQKWNLEAEKEDDELDSKEEFKEKLVSFCSQPSVNPSPQANGEIDLLASGSVTESQCFSSLAEVSLPL
          EINQKWNLEAEKEDDELDSKEEFKEKLVSFCSQPSVNP.PQANGEIDLLASGSVTESQCFSSLAEVSLPL
Retrocopy EINQKWNLEAEKEDDELDSKEEFKEKLVSFCSQPSVNPNPQANGEIDLLASGSVTESQCFSSLAEVSLPL

Parental  AEQIESPELESRNEELTPQKNLCENPLPPKQSLPSGHSGRRGRRSSRSSPISKRCRSSIPGTSSQHIVLS
          AEQIESPELESRNEELTPQKNLCENPLPPKQSLPSGHSG.RG..SSRSSPISKRCRSSIPGTSSQHIVLS
Retrocopy AEQIESPELESRNEELTPQKNLCENPLPPKQSLPSGHSGHRGQHSSRSSPISKRCRSSIPGTSSQHIVLS

Parental  ESKPLPGCSSPPSSKLKIGDTLRRKNSNLSVESMTLSPGTPPSALNSPRYRRMMSSPSATKLSPNSLTAV
          E.KPLPGCSSPPSSKLKIGDTLRRKNSNLSVESMTLSPGTPPSALN.P.YRRMMSSPSATKLSPNSLTAV
Retrocopy ENKPLPGCSSPPSSKLKIGDTLRRKNSNLSVESMTLSPGTPPSALNNPSYRRMMSSPSATKLSPNSLTAV

Parental  KRNHRGETLLHIASIKGDVPSVEYLLQNGSDPNVKDHAGWTPLHEACNHGHLKVVELLLQHQALVNTPGY
          KRNHRGETLLHIASIKGDVPSVEYLLQNGSDPNVKDHAGWTPLHEACNH.HLKVVELL.QHQALVNTPGY
Retrocopy KRNHRGETLLHIASIKGDVPSVEYLLQNGSDPNVKDHAGWTPLHEACNHRHLKVVELLVQHQALVNTPGY

Parental  QNDSPLHDAARNGHLEIVKLLLASGASRDAVNIFGLRPVDYADNENMKSLLLLPEKNESSSTRHYSVPNT
          QNDSPLH.AARNGHLEIVKLLLASGASRDA.NIFGLRPVDYADNENMKSLLLLPEKNESSSTRHYSVPNT
Retrocopy QNDSPLHNAARNGHLEIVKLLLASGASRDAINIFGLRPVDYADNENMKSLLLLPEKNESSSTRHYSVPNT

Parental  GQRRDGPLVLIGSGLSSEQQKMLSELAAILKAKKCAEFDNTVTHVIVPGDTVQSTLKCMLGILNGCWILK
          GQRRDGPLVLIGSGLSSE.QKMLSELAAILKAKKCAEFDNTVTHVIVPGDTVQSTLKCMLGILNGCWILK
Retrocopy GQRRDGPLVLIGSGLSSE-QKMLSELAAILKAKKCAEFDNTVTHVIVPGDTVQSTLKCMLGILNGCWILK

Parental  FEWVKACLQRKACEQEEKYEIPEGPHRSRLNKEQLLPKLFDGCYFYFGGTFKHHPKDNLIKLVTAAGGQV
          FEWVKACLQRKACEQEEKYEIPEGPHRSRLNKEQLLPKLFDGCYFYFGGTFKHHPKDNLIKLVTAAGGQV
Retrocopy FEWVKACLQRKACEQEEKYEIPEGPHRSRLNKEQLLPKLFDGCYFYFGGTFKHHPKDNLIKLVTAAGGQV

Parental  LSRKPKPDSDVTQTINTVAYHARPDSDQRFCTQYIIYEDLSNHHPKRVRQGKVWMAPSSWFIDCVMSFEL
          LSRKPKPDSDVTQTINTVAYHARPDSDQRFCTQYIIYEDLSNHHPKRVRQGKVWMAPSSWFIDCVMSFEL
Retrocopy LSRKPKPDSDVTQTINTVAYHARPDSDQRFCTQYIIYEDLSNHHPKRVRQGKVWMAPSSWFIDCVMSFEL

Parental  LPLDS
          LPLDS
Retrocopy LPLDS

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	5.42 RPM
SRP017611_brain	0.00 RPM	1.98 RPM
SRP017611_kidney	0.07 RPM	9.44 RPM
SRP017611_liver	0.29 RPM	15.66 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1930 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1930 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1930 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	ENSCAFG00000014264	1 retrocopy	retro_cfam_1930 ,