RetrogeneDB ID: retro_cfam_936

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:46760594..46761582(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4B
• Ensembl ID: ENSCAFG00000007117
• Aliases: None
• Description: eukaryotic translation initiation factor 4B [Source:HGNC Symbol;Acc:3285]

Sequence

>retro_cfam_936
CGTCCTGCCACAGACAGCTTCGATGACTACCCACCTAGGAGAGGTGATGATAGCTTTGGAGACAAGGATCGAGACCGTTA
CGATTCAGACTGATACCGTGATGGATATCGGGATGGGTATCGTGATGGTCCACGCCGAGATATGGACCGATACGGAGGCC
GGGATCGCTATAATGACCGAGGCAGCCGAGACTATGACAGAGGCTACGATTCCAGGATAGGCAGTGGCAGAAGAGCATTT
GGTAGTGGGTACCGAAGGGATGACGACTACAGAGGAGGCGGGGACCGCTATGAAGACAGATACGACAGGCGAGACAACCG
GTCCTGGAGCTCCAGAGATGATTACTCTCGGGATGACTATAGGCGTGATGATAGAGGTCCCCCCCAAAGACCCAAACTGA
ATCTAAAGCCTCGGAGTACTCCTAAGGAAGATGATTCCTCCGCTAGCACCTCCCAGTCTCGTCGAGCGGCCTCTATCTTT
GGAGGGGCAAAGCCTGTTGACACAGCTGCTAGAGAGTGAGAAGTAGAAGAGCGGCTGCAGAAGGAGCAGGAGAAGCTGCA
GCACCAGCTGGATGAGCCAAAACTAGAGCGACGGCCTCGAGAGAGACACCCAAGCTGGCGAAGTGAAGAGACTCAGGAAC
GCGAACGGTCCAGGACAGGAAGTGAGTCATCACAGACTGGAACCTCGGCCACAACTGGCAGAAGTAAGTCAGACCAGGAT
GCATGAAGGAGAGAGAGAGTGAGAAGTCTCTAGAAAATAAAACACCGAATAAGGAGGAAGACTGTCACTCTCCAACTTCT
AAGCCACCCAAATCTGAACAGCCTCTGAAGGTAATGCCAGCCCCTCCACCAAAGGAGAATGCTTGGGTGAAGCGAAGTTC
TAACCCTCCTGCCCGATCTCAGAGCTCGGACACAGAGCAAAAGTCCCCCACGAGTGGTGGAGAGAAAGCAGTCCCGGCTC
AGCCCCGGAGGAAGGACCAGCAAGGAGA

Alignment

ORF - retro_cfam_936 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.18 %
• Parental protein coverage: 52.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RPATDSFDDYPPRRGDDSFGDKYRDRYDSDRYRDGYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYD
          RPATDSFDDYPPRRGDDSFGDK.RDRYDSD.............PRRDMDRYGGRDRY.DRGSRDYDRGYD
Retrocopy RPATDSFDDYPPRRGDDSFGDKDRDRYDSDXXXXXXXXXXXXXPRRDMDRYGGRDRYNDRGSRDYDRGYD

Parental  SRIGSGRRAFGSGYRRDDDYRGGGDRYEDRYDRRDDRSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRST
          SRIGSGRRAFGSGYRRDDDYRGGGDRYEDRYDRRD.RSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRST
Retrocopy SRIGSGRRAFGSGYRRDDDYRGGGDRYEDRYDRRDNRSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRST

Parental  PKEDDSSASTSQSSRAASIFGGAKPVDTAAR----EREVEERLQKEQEKLQR-QLDEPKLERRPRERHPS
          PKEDDSSASTSQS.RAASIFGGAKPVDTAAR....E........K.Q..L....L.....ER.P..R...
Retrocopy PKEDDSSASTSQSRRAASIFGGAKPVDTAARE*EVEERLQKEQEKLQHQLDEPKLERRPRERHPSWRSEE

Parental  WRSEETQER--ERSRTGSESSQTGTSATTGRNARR-RESEKSLENETPNKEEDCHSPTSKPPKSEQPLKV
          ....E......E.S.TG..S..TG.S.......RR.RESEKSLEN.TPNKEEDCHSPTSKPPKSEQPLKV
Retrocopy TQERERSRTGSESSQTGT-SATTGRSKSDQDA*RR<RESEKSLENKTPNKEEDCHSPTSKPPKSEQPLKV

Parental  MPAPPPKENAWVKRSSNPPARSQSSDTEQQSPTSGGGKAVPAQP-PEEGPARR
          MPAPPPKENAWVKRSSNPPARSQSSDTEQ.SPTSGG.KAVPAQP.PEEGPARR
Retrocopy MPAPPPKENAWVKRSSNPPARSQSSDTEQKSPTSGGEKAVPAQP<PEEGPARR

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	0.59 RPM	226.16 RPM
SRP017611_brain	0.08 RPM	109.32 RPM
SRP017611_kidney	1.98 RPM	443.97 RPM
SRP017611_liver	2.03 RPM	426.02 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_936 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_936 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_936 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012023	2 retrocopies	retro_amel_1107, retro_amel_559,
Canis familiaris	ENSCAFG00000007117	2 retrocopies	retro_cfam_1447, retro_cfam_936 ,
Choloepus hoffmanni	ENSCHOG00000001608	2 retrocopies	retro_chof_1310, retro_chof_366,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Tarsius syrichta	ENSTSYG00000012880	1 retrocopy	retro_tsyr_452,