RetrogeneDB ID: retro_cfam_1095

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 23:3616258..3617467(+)
• Located in intron of: ENSCAFG00000029974

Retrocopy information

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

Parental gene information

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

Sequence

>retro_cfam_1095
ATGGCAGACCCCAAATACGCCGACCTTCCCGGCATTGCCAGGAACGAGCCAGATGTTTATGAAACCAGCGACCTACCTGA
AGATGATCAAGCAGAGTTTGATGCGGAGGAGCTGACGAGCACAAGTGTGGAGCACATCATTGTCAATCCCAATGCTGCCT
ATGACAAGTTCAAAGACAAGAGAGTGGGGACAAAGGGACTTGATTTCTCAGATCGTATTGGAAAAACCAAGAGAACAGGA
TATGAATCTGGAGAATATGAGATACTTGGAGAGGGTCTAGGAGTGAAGGAGACACCCCAGCAAAAGTACCAGCGACTACT
GCATGAGGTCCAAGAGCTGACAACTGAAGTTGAGAAAATCAAGACATCGGTGAAGGAGTCAGCCACTGAAGAGAAGCTGA
CCCCAGTGGTTTTGGCTAAGCAGCTGGCAGCCTTGAAGCAGCAGCTGGTTGCTTCCCACCTGGAGAAGCTGCTGGGACCA
GATGCAGCTATCAACCTTACTGACCCTGATGGAGCTCTGGCTAAGCGCCTGCTGCTGCAGCTGGAAGCAACAAAAAACAG
CAAAGGAACTGGTTCAGGGGGAAAGACCACCGGTGGGACTCCCGTAGATAGTAACCTTGTCACTTACGAACTACATTCTC
GGCCTGAACAGGACAAGTTCTCTCAAGCTGCCAAAGTTGCAGAACTTGAGAAGCGCCTGACAGAGCTGGAAGCCACTGTA
CGCTGTGATCAGGACGCTCAGAATCCCCTTTCAGCAGGTCTACAGGGAGCCTGTCTTATGGAGACTGTAGAACTGTTGCA
AGCAAAGGTGAACGCCCTGGACCTCGCAGTTCTGGACCAAGTGGAGGCTCGGCTACAGAGTGTCCTGGGCAAGGTGAACG
AGATTGCCAAGCATAAAGCTTCTGTAGAGGATGCAGATACACAAAGCAAGGTGCACCAGCTCTATGAAACCATACAGCGC
TAGAGCCCCATCGCCTCCACCCTGCCTGAGCTGGTGCAGAGACTTGTCACCATCAAGCAGCTGCATGAGCAAGCCATGCA
GTTCGGTCAGCTCCTGACACACTTGGATACCACACAGCAGATGATTGCTAGCTCCCTCAAGGACAACACCGCCCTCCTGA
CCCAAGTGCAGACAACCATGCGTGAGAACCTGTCCACAATTGAGGGGAATTTTGCCAACATTGATGAGCGGATGAAGCAG
CTGGGAAAG

Alignment

ORF - retro_cfam_1095 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADPKYADLPGIARNEPDVYETSDLPEDDQAEFDAEELTSTSVEHIIVNPNAAYDKFKDKRVGTKGLDFS
          MADPKYADLPGIARNEPDVYETSDLPEDDQAEFDAEELTSTSVEHIIVNPNAAYDKFKDKRVGTKGLDFS
Retrocopy MADPKYADLPGIARNEPDVYETSDLPEDDQAEFDAEELTSTSVEHIIVNPNAAYDKFKDKRVGTKGLDFS

Parental  DRIGKTKRTGYESGEYEMLGEGLGVKETPQQKYQRLLHEVQELTTEVEKIKTSVKESATEEKLTPVVLAK
          DRIGKTKRTGYESGEYE.LGEGLGVKETPQQKYQRLLHEVQELTTEVEKIKTSVKESATEEKLTPVVLAK
Retrocopy DRIGKTKRTGYESGEYEILGEGLGVKETPQQKYQRLLHEVQELTTEVEKIKTSVKESATEEKLTPVVLAK

Parental  QLAALKQQLVASHLEKLLGPDAAINLTDPDGALAKRLLLQLEATKNSKGTGSGGKTTGGTPVDSNLVTYE
          QLAALKQQLVASHLEKLLGPDAAINLTDPDGALAKRLLLQLEATKNSKGTGSGGKTTGGTPVDSNLVTYE
Retrocopy QLAALKQQLVASHLEKLLGPDAAINLTDPDGALAKRLLLQLEATKNSKGTGSGGKTTGGTPVDSNLVTYE

Parental  LHSRPEQDKFSQAAKVAELEKRLTELEATVRCDQDAQNPLSAGLQGACLMETVELLQAKVNALDLAVLDQ
          LHSRPEQDKFSQAAKVAELEKRLTELEATVRCDQDAQNPLSAGLQGACLMETVELLQAKVNALDLAVLDQ
Retrocopy LHSRPEQDKFSQAAKVAELEKRLTELEATVRCDQDAQNPLSAGLQGACLMETVELLQAKVNALDLAVLDQ

Parental  VEARLQSVLGKVNEIAKHKASVEDADTQSKVHQLYETIQRWSPIASTLPELVQRLVTIKQLHEQAMQFGQ
          VEARLQSVLGKVNEIAKHKASVEDADTQSKVHQLYETIQR.SPIASTLPELVQRLVTIKQLHEQAMQFGQ
Retrocopy VEARLQSVLGKVNEIAKHKASVEDADTQSKVHQLYETIQR*SPIASTLPELVQRLVTIKQLHEQAMQFGQ

Parental  LLTHLDTTQQMIASSLKDNTALLTQVQTTMRENLSTIEGNFANIDERMKQLGK
          LLTHLDTTQQMIASSLKDNTALLTQVQTTMRENLSTIEGNFANIDERMKQLGK
Retrocopy LLTHLDTTQQMIASSLKDNTALLTQVQTTMRENLSTIEGNFANIDERMKQLGK

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	71.36 RPM
SRP017611_brain	1.83 RPM	71.77 RPM
SRP017611_kidney	0.26 RPM	53.03 RPM
SRP017611_liver	0.22 RPM	29.95 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1095 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1095 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1095 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,