RetrogeneDB ID: retro_cfam_1510

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:33879985..33880588(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000032678
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB2B
• Ensembl ID: ENSCAFG00000005641
• Aliases: None
• Description: RAB2B, member RAS oncogene family [Source:HGNC Symbol;Acc:20246]

Sequence

>retro_cfam_1510
TCAGGCGTGGGCAAGTCATGTCTCCTCCTGCAGTTCACGGACAAGCGGTTCCAGCCGGTGCACGACCTCACCATAGGTGT
GGAGTTTGGGGCCCGTATGGTCAACATTGATGGAAAACAAATCAAACTGCAAATCTGGGACACGGCTGGGCAAGAATCCT
TCCGTTCTATCACCCGTTCCTACTACAGGGGAGCAGCTGGAGCACTGCTAGTATATGACATCACAAGGCGTGAAACCTTC
AACCACCTGACCTCCTGGTTAGAGGATGCCCGGCAACACTCCAGCTCCAACATGGTTATCATGCTGATTGGGAATAAGAG
TGACTTAGAATCCCGTAGGGATGTGAAGAGAGAAGGAGAGGCCTTTGCCCGGGAGCATGGACTTATCTTCATGGAAACTT
CAGCCAAAACAGCCTGCAATGTTGAAGAGGCCTTCATTAACACAGCCAAAGAAATATATAGGAAGATCCAGCAGGGTTTA
TTTGATGTCCACAATGAGGCGAATGGCATCAAGATTGGTCCTCAGCAGTGTATTTCAACATCAGTAGGACCCAGTGCCTC
CCAGCGGAGCTCTAATGAAATAGGGTCCAACTCTGGCTGCTGC

Alignment

ORF - retro_cfam_1510 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.51 %
• Parental protein coverage: 93.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMVNIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGALL
          .GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMVNIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGALL
Retrocopy SGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMVNIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGALL

Parental  VYDITRRETFNHLTSWLEDARQHSSSNMVIMLIGNKSDLESRRDVKREEGEAFAREHGLIFMETSAKTAC
          VYDITRRETFNHLTSWLEDARQHSSSNMVIMLIGNKSDLESRRDVKRE.GEAFAREHGLIFMETSAKTAC
Retrocopy VYDITRRETFNHLTSWLEDARQHSSSNMVIMLIGNKSDLESRRDVKRE-GEAFAREHGLIFMETSAKTAC

Parental  NVEEAFINTAKEIYRKIQQGLFDVHNEANGIKIGPQQCISASVGPSASQRSSNEIGSNSGCC
          NVEEAFINTAKEIYRKIQQGLFDVHNEANGIKIGPQQCIS.SVGPSASQRSSNEIGSNSGCC
Retrocopy NVEEAFINTAKEIYRKIQQGLFDVHNEANGIKIGPQQCISTSVGPSASQRSSNEIGSNSGCC

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	0.42 RPM	21.04 RPM
SRP017611_brain	0.32 RPM	28.10 RPM
SRP017611_kidney	0.26 RPM	9.18 RPM
SRP017611_liver	0.00 RPM	2.18 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1510 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1510 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1510 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000044207	1 retrocopy	retro_btau_991,
Canis familiaris	ENSCAFG00000005641	1 retrocopy	retro_cfam_1510 ,
Canis familiaris	ENSCAFG00000007153	1 retrocopy	retro_cfam_2057,
Choloepus hoffmanni	ENSCHOG00000000710	3 retrocopies	retro_chof_2314, retro_chof_706, retro_chof_900,
Cavia porcellus	ENSCPOG00000026575	1 retrocopy	retro_cpor_839,
Macropus eugenii	ENSMEUG00000010489	2 retrocopies	retro_meug_2160, retro_meug_91,
Myotis lucifugus	ENSMLUG00000001902	3 retrocopies	retro_mluc_1243, retro_mluc_1251, retro_mluc_2103,
Sorex araneus	ENSSARG00000004969	1 retrocopy	retro_sara_97,
Ictidomys tridecemlineatus	ENSSTOG00000001886	1 retrocopy	retro_itri_468,