RetrogeneDB ID: retro_cfam_1579

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 35:8365439..8366114(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDE1
• Ensembl ID: ENSCAFG00000018722
• Aliases: None
• Description: Canis lupus familiaris nudE nuclear distribution gene E homolog 1 (A. nidulans) (NDE1), mRNA. [Source:RefSeq mRNA;Acc:NM_001252172]

Sequence

>retro_cfam_1579
ATGGAAGACTCGGGAAAGACTTTCAGTTCTGAGGAGGAAGAAGTGAACTACTGGAAAGATCTGGCTATGACCTACAAGCA
GAGGGCAGAGAACACGCAGGAGGAACTCCGAGAATTCCAGGAGGGAAGCCGCGAATATGATGCTGAACTGGAGACGCAGC
TGCAACAGATTGAAACCAGGAACAGGGACCTCCTGTCGGAGAATAACCGCCTTCGTATGGAGCTGGAAACCATCAAGGAG
AAGTTTGAAACTCAGCACTCCGAAGGCTACCGGCAGATTTCAGCCTTGGAGGATGACCTTGCCCAGACCAAAGCAATTAA
GGATCAACTTCAGAAATACATCAGAGAGCTGGAGCAAGCAAATGACGACTTGGAAAGAGCAAAACGGGCCACGATCATGT
CTCTGGAAGACTTTGAGCAGCGTTTGAATCAAGCCATTGAAAGAAATGCCTTCCTGGAGAGTGAGCTTGATGAGAAAGAG
AATCTCCTAGAATCTGTTCAGCGACTGAAGGATGAAGCCAGAGATTTGCGGCAGGAGTTGGCTGTGCAGCAGAAGCAGGA
GAAGCCCCGGACCCCCATGCCTACCTCGGTGGAAGCCGAAAGGACAGACACAGCTGTGCAGGCCACTGGCTCTGTACCAT
CCACTCCCATAGCGCATCGGGGACCCAGCACTAGC

Alignment

ORF - retro_cfam_1579 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.67 %
• Parental protein coverage: 67.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDSGKTFSSEEEEANYWKDLAMTYKQRAENTQEELREFQEGSREYEAELETQLQQIETRNRDLLSENNR
          MEDSGKTFSSEEEE.NYWKDLAMTYKQRAENTQEELREFQEGSREY.AELETQLQQIETRNRDLLSENNR
Retrocopy MEDSGKTFSSEEEEVNYWKDLAMTYKQRAENTQEELREFQEGSREYDAELETQLQQIETRNRDLLSENNR

Parental  LRMELETIKEKFETQHSEGYRQISALEDDLAQTKAIKDQLQKYIRELEQANDDLERAKRATIMSLEDFEQ
          LRMELETIKEKFETQHSEGYRQISALEDDLAQTKAIKDQLQKYIRELEQANDDLERAKRATIMSLEDFEQ
Retrocopy LRMELETIKEKFETQHSEGYRQISALEDDLAQTKAIKDQLQKYIRELEQANDDLERAKRATIMSLEDFEQ

Parental  RLNQAIERNAFLESELDEKENLLESVQRLKDEARDLRQELAVQQKQEKPRTPMPSSVEAERTDTAVQATG
          RLNQAIERNAFLESELDEKENLLESVQRLKDEARDLRQELAVQQKQEKPRTPMP.SVEAERTDTAVQATG
Retrocopy RLNQAIERNAFLESELDEKENLLESVQRLKDEARDLRQELAVQQKQEKPRTPMPTSVEAERTDTAVQATG

Parental  SVPSTPIAHRGPSTS
          SVPSTPIAHRGPSTS
Retrocopy SVPSTPIAHRGPSTS

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	5.46 RPM
SRP017611_brain	0.00 RPM	8.02 RPM
SRP017611_kidney	0.00 RPM	3.17 RPM
SRP017611_liver	0.00 RPM	1.52 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1579 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1579 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1579 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009557	1 retrocopy	retro_amel_104,
Canis familiaris	ENSCAFG00000018722	1 retrocopy	retro_cfam_1579 ,
Choloepus hoffmanni	ENSCHOG00000006004	1 retrocopy	retro_chof_1270,
Cavia porcellus	ENSCPOG00000019614	2 retrocopies	retro_cpor_875, retro_cpor_876,
Ictidomys tridecemlineatus	ENSSTOG00000019896	1 retrocopy	retro_itri_1101,
Tupaia belangeri	ENSTBEG00000005260	1 retrocopy	retro_tbel_1468,