RetrogeneDB ID: retro_cfam_2057

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:35098827..35099522(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000014123
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB2A
• Ensembl ID: ENSCAFG00000007153
• Aliases: RAB2A, RAB2
• Description: Canis lupus familiaris RAB2A, member RAS oncogene family (RAB2A), mRNA. [Source:RefSeq mRNA;Acc:NM_001003318]

Sequence

>retro_cfam_2057
AGAAGGAGGAGGAGCAGGGGCCGGAGGAGGAGCCGTGTGCCCAGACACCGAACGCCATGGCCTACGCCTATCTCTTCAAG
TACATCATCATCGGCGACACGGGTGTTGGTAAATCATGCTTATTGCTGCAGTTTACGGACAAGAGGTTTCAGCCAGTGCA
TGACCTGACTATCGGTGTAGAGTTTGGCGCTCGAATGATAACTATCGATGGGAAACGGATAAAACTTCAGATATGGGATA
CGGCAGGGCAAGAGTCCTTTCGTTCCATCACGAGGTCATATTACAGAGGCGCGGCAGGGGCGTTACTAGTGTATGATATC
ACAAGGAGAGATACATTCAACCACTTGACAACCTGGTTGGAAGATGCCCGCCATTATTCCAATTCCAACATGGTCATTAT
GCTTATTGGCAATAAAAGTGATTTAGAATCTAGAAGGGAAGTAAACAAAGAGGAAGGGGAAGCTTTTGCACGAGAACATG
GACTTATCTTCATGGAAACTTCTGCTAAGACTGCCTCCAATGTAGAAGAGGCATTTATTAATACAGCAAAAGAAATCTAT
GAGAAAATCCAAGAAGGAGTCCTTGACATTAACAACGAGGCAAATGGTGTTAAAATTGGCCTTCAGCACGCTGCTGCTAC
TAATGCCATACATGTAGGCCATCACGGAGGACAGCAGGGCGGGGGAGGCTGCTGT

Alignment

ORF - retro_cfam_2057 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.27 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRSRSGRRSRV-PWHRASAAMAYAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITI
          RR.RS..R.R..P......AMAYAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITI
Retrocopy RRRRSRGRRRS<PCAQTPNAMAYAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITI

Parental  DGKQIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRDTFNHLTTWLEDARQHSNSNMVIMLIGNK
          DGK.IKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRDTFNHLTTWLEDAR..SNSNMVIMLIGNK
Retrocopy DGKRIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRDTFNHLTTWLEDARHYSNSNMVIMLIGNK

Parental  SDLESRREVKKEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEIYEKIQEGVFDINNEANGIKIGPQ
          SDLESRREV.KEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEIYEKIQEGV.DINNEANG.KIG.Q
Retrocopy SDLESRREVNKEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEIYEKIQEGVLDINNEANGVKIGLQ

Parental  H-AATNATHAGNQGGQQAGGGCC
          H.AATNA.H.G..GGQQ.GGGCC
Retrocopy HAAATNAIHVGHHGGQQGGGGCC

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	199.03 RPM
SRP017611_brain	0.08 RPM	151.96 RPM
SRP017611_kidney	0.20 RPM	146.93 RPM
SRP017611_liver	0.00 RPM	45.03 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2057 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2057 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2057 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005641	1 retrocopy	retro_cfam_1510,
Canis familiaris	ENSCAFG00000007153	1 retrocopy	retro_cfam_2057 ,
Equus caballus	ENSECAG00000012124	1 retrocopy	retro_ecab_970,
Monodelphis domestica	ENSMODG00000008556	2 retrocopies	retro_mdom_1999, retro_mdom_989,
Sorex araneus	ENSSARG00000013511	2 retrocopies	retro_sara_688, retro_sara_744,
Tarsius syrichta	ENSTSYG00000013060	1 retrocopy	retro_tsyr_1215,
Tursiops truncatus	ENSTTRG00000009615	1 retrocopy	retro_ttru_1377,