RetrogeneDB ID: retro_cfam_385

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:40514312..40515522(-)
• Located in intron of: ENSCAFG00000002130

Retrocopy information

• Ensembl ID: ENSCAFG00000002132
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cfam_385
ATGGCGGACCCCAAATACACTGACCTTCCCGGCATTGCCAGGAATGAGCCAGATGTTTATGGAACCAGCGACCTACCTGA
GGATGATCAAGCAGAGTTTGATGCGGAGGAGTTGACGAGCACAAGTGTGGAGCACATCATTGTCAATTCCAATGCTGCCT
ATGACAAGTTCAAAGACAAGAGAGTGGGGACAAAGGGACTTGATTTCTCAGATCGTATTGGAAAAACCAAGAGAACAGGA
TATGAATCTGGAGAATATGAGATGCTTGGAGAGGGTCTAGGAGTGAAGGAGACACCCCAGCAAAAATACCAGCGACTACT
GCATGAGGTCCAAGAGCTGACAGCTGAAGTTGAGAAAATCAAGACAACGGTGAAGGAGTCAGCCACTGAAGAGGAGCTGA
CCCCAGTGGTTTTGGCTAAGCAGCTGGCAGCCCTGAAGCAGCAGCTGGTTGCTTCCCACCTGGAGAAGCTGCTGGGACCA
GATGTAGCTATCGACCCTACTGACCCTGATGGAGCTCTGGCTAAGTGCCTACTGCTGCAGCTGGAAGCAACAAAAAACAG
CAAAGGAACTGGTTCAGGGGGAAAGACCACTGGTGGGACTCCCGTAGATAGTAACCTTGTCACTTACGAACTACATTCTC
GGCTTGAACAGGACAAGTTCTCTCAAGCTGCCAAAGTTGCAGAACTTGAGAAGTGCCTGACAGAGCTGGAAGCCACTGTA
CGCTGTGATCAGGATGCTCAGAATCCCCTTTCAGCAGGTCTACAGGGAACCTGTCTTATGGAGACCGTAGAACTGTTGCA
AGCAAAGGTGAATGCCCTCGACCTCGCAGTTCTGGACCAAGTGGAGGCTCAGCTACAGAGTGTCCTGGGCAAGGTGAATG
AGATTGCCAAGCATAAAGCTTCTGTAGAGGATGCAGATACAGAAAGCAAGGTGCACCAGCTCTATGAAACCATACAGCGC
TGGAGCCCCATCGCCTGCACCCTTCCTGAGCTGGTGCAGAGGCTTGTCACCATCAAGCAGCTGCATGAGCAAGCCTTGCA
GTTTGGTCAGCTCCTGACACACTTGGGATACCACACAGCAGATGATCCCTAGCTCCCTCAAGGACAACACCGCCCTCCTG
ACCCAGGTGCAGACAACCATGCGTGAGAACCTGTCCACAACTGAGGGGAATTTTGCCAACATCCATGAGTGGATGAAGCA
GCTGGGAAAG

Alignment

ORF - retro_cfam_385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.55 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADPKYADLPGIARNEPDVYETSDLPEDDQAEFDAEELTSTSVEHIIVNPNAAYDKFKDKRVGTKGLDFS
          MADPKY.DLPGIARNEPDVY.TSDLPEDDQAEFDAEELTSTSVEHIIVN.NAAYDKFKDKRVGTKGLDFS
Retrocopy MADPKYTDLPGIARNEPDVYGTSDLPEDDQAEFDAEELTSTSVEHIIVNSNAAYDKFKDKRVGTKGLDFS

Parental  DRIGKTKRTGYESGEYEMLGEGLGVKETPQQKYQRLLHEVQELTTEVEKIKTSVKESATEEKLTPVVLAK
          DRIGKTKRTGYESGEYEMLGEGLGVKETPQQKYQRLLHEVQELT.EVEKIKT.VKESATEE.LTPVVLAK
Retrocopy DRIGKTKRTGYESGEYEMLGEGLGVKETPQQKYQRLLHEVQELTAEVEKIKTTVKESATEEELTPVVLAK

Parental  QLAALKQQLVASHLEKLLGPDAAINLTDPDGALAKRLLLQLEATKNSKGTGSGGKTTGGTPVDSNLVTYE
          QLAALKQQLVASHLEKLLGPD.AI..TDPDGALAK.LLLQLEATKNSKGTGSGGKTTGGTPVDSNLVTYE
Retrocopy QLAALKQQLVASHLEKLLGPDVAIDPTDPDGALAKCLLLQLEATKNSKGTGSGGKTTGGTPVDSNLVTYE

Parental  LHSRPEQDKFSQAAKVAELEKRLTELEATVRCDQDAQNPLSAGLQGACLMETVELLQAKVNALDLAVLDQ
          LHSR.EQDKFSQAAKVAELEK.LTELEATVRCDQDAQNPLSAGLQG.CLMETVELLQAKVNALDLAVLDQ
Retrocopy LHSRLEQDKFSQAAKVAELEKCLTELEATVRCDQDAQNPLSAGLQGTCLMETVELLQAKVNALDLAVLDQ

Parental  VEARLQSVLGKVNEIAKHKASVEDADTQSKVHQLYETIQRWSPIASTLPELVQRLVTIKQLHEQAMQFGQ
          VEA.LQSVLGKVNEIAKHKASVEDADT.SKVHQLYETIQRWSPIA.TLPELVQRLVTIKQLHEQA.QFGQ
Retrocopy VEAQLQSVLGKVNEIAKHKASVEDADTESKVHQLYETIQRWSPIACTLPELVQRLVTIKQLHEQALQFGQ

Parental  LLTHL-DTTQQMIASSLKDNTALLTQVQTTMRENLSTIEGNFANIDERMKQLGK
          LLTHL.DTTQQMI.SSLKDNTALLTQVQTTMRENLST.EGNFANI.E.MKQLGK
Retrocopy LLTHL>DTTQQMIPSSLKDNTALLTQVQTTMRENLSTTEGNFANIHEWMKQLGK

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	71.36 RPM
SRP017611_brain	0.00 RPM	71.77 RPM
SRP017611_kidney	0.00 RPM	53.03 RPM
SRP017611_liver	0.00 RPM	29.95 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_385 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_385 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_385 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,