RetrogeneDB ID: retro_cfam_579

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:49517624..49518640(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000002333
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DCTN2
• Ensembl ID: ENSCAFG00000000233
• Aliases: None
• Description: None

Sequence

>retro_cfam_579
CTTGATTTCTCAGATCGTATTGGAAAAACCAAGAGAACAGGATATGAATCTGGAGAATATGAGATGCTTGGAGAGGGTCT
AGGAGTGAAGGAGACACCCCAGCAAAAGTACCAGCAACTACTGCATGAGGTCCAAGAGCTGACAACTGAAGTTGAGAAAA
TCAAGACAACGGTGAAGGAGTCAGCCACTGAAGAGAAGCTGACCCCAGTGGTTTTGGCTAAGCAGCTGGCAGCCCTGAAG
CAGCAGCTGGTTGCTTCCCACCTGGAGAAGCTGCTGGGACCAGATGCAGCTATCAACCTTACTGACCCTGATGGAGCTCT
GGCTAAGCACCTGCTGCTGCAGCTAGAAGCAACAAAAAAACAGCAAAGGAACTGGTTCAGGGGGAAAGACCACTGGTGGG
ACTCCCATAGATAGTAAGTAACCTTGTCACTTACGAACTACATTCTCAGCCTGAACAGGACAAGTTCTCTCAAGCTGCCA
AAGTTGCAGAACTTGAGAAGTGCCTGACAGAGCTGGAAGCCACTGTACGCCGTGATCAGGACGCTCAGAATCCCCTTTCA
GCAGGTCTACAGGGAGCCTGTCTTATGGAGACCGTAGAACTGTTGCAAGCAAAGGTGAACACCCTGGACCTCACAGTTCT
GGACCAAGTGGAGGCTCGACTACAGAGTGTCCTGGGCAAGGTGAACGAGATTGCCAAGCATAAAGCTTCTGTAGAGGATG
CAGATACACAAAGCAGGGTGCACCAGCTCTATGAAACCATACAGCGCTGGAGCCCCATCGCCTCCACCCTGCCTGAGCTG
GTGCAGAGACTTGTCACCATCAAGCAGCTGCATGAGCAAGCCACGCAGTTCGGTCAGCTCCTGACACACTTGGATACCAC
ACAGCAGATGATTGCTAGCTCCCTCAAGGACAACACCGCCCTCCTGACCCAGGTGCAGACAACCATGCGTGAGAACCTGT
CCACAATTGAGGGGAATTTTGCCAACATCAATGAGCGGATGAAGCAGCTGGGAAAG

Alignment

ORF - retro_cfam_579 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.0 %
• Parental protein coverage: 83.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LDFSDRIGKTKRTGYESGEYEMLGEGLGVKETPQQKYQRLLHEVQELTTEVEKIKTSVKESATEEKLTPV
          LDFSDRIGKTKRTGYESGEYEMLGEGLGVKETPQQKYQ.LLHEVQELTTEVEKIKT.VKESATEEKLTPV
Retrocopy LDFSDRIGKTKRTGYESGEYEMLGEGLGVKETPQQKYQQLLHEVQELTTEVEKIKTTVKESATEEKLTPV

Parental  VLAKQLAALKQQLVASHLEKLLGPDAAINLTDPDGALAKRLLLQLEATK-NSKGTGSGGKTTG-GTP-VD
          VLAKQLAALKQQLVASHLEKLLGPDAAINLTDPDGALAK.LLLQLEATK.NSKGTGSGGKTTG.G.P...
Retrocopy VLAKQLAALKQQLVASHLEKLLGPDAAINLTDPDGALAKHLLLQLEATK>NSKGTGSGGKTTG>GLP*IV

Parental  SNLVTYELHSRPEQDKFSQAAKVAELEKRLTELEATVRCDQDAQNPLSAGLQGACLMETVELLQAKVNAL
          SNLVTYELHS.PEQDKFSQAAKVAELEK.LTELEATVR.DQDAQNPLSAGLQGACLMETVELLQAKVN.L
Retrocopy SNLVTYELHSQPEQDKFSQAAKVAELEKCLTELEATVRRDQDAQNPLSAGLQGACLMETVELLQAKVNTL

Parental  DLAVLDQVEARLQSVLGKVNEIAKHKASVEDADTQSKVHQLYETIQRWSPIASTLPELVQRLVTIKQLHE
          DL.VLDQVEARLQSVLGKVNEIAKHKASVEDADTQS.VHQLYETIQRWSPIASTLPELVQRLVTIKQLHE
Retrocopy DLTVLDQVEARLQSVLGKVNEIAKHKASVEDADTQSRVHQLYETIQRWSPIASTLPELVQRLVTIKQLHE

Parental  QAMQFGQLLTHLDTTQQMIASSLKDNTALLTQVQTTMRENLSTIEGNFANIDERMKQLGK
          QA.QFGQLLTHLDTTQQMIASSLKDNTALLTQVQTTMRENLSTIEGNFANI.ERMKQLGK
Retrocopy QATQFGQLLTHLDTTQQMIASSLKDNTALLTQVQTTMRENLSTIEGNFANINERMKQLGK

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	0.13 RPM	71.36 RPM
SRP017611_brain	0.24 RPM	71.77 RPM
SRP017611_kidney	0.13 RPM	53.03 RPM
SRP017611_liver	0.07 RPM	29.95 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_579 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_579 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_579 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000233	3 retrocopies	retro_cfam_1095, retro_cfam_385, retro_cfam_579 ,
Dipodomys ordii	ENSDORG00000007137	1 retrocopy	retro_dord_441,
Loxodonta africana	ENSLAFG00000013538	1 retrocopy	retro_lafr_312,
Mustela putorius furo	ENSMPUG00000001840	1 retrocopy	retro_mputfur_197,
Procavia capensis	ENSPCAG00000016236	1 retrocopy	retro_pcap_430,