RetrogeneDB ID: retro_cfam_1447

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 31:16835193..16836275(-)
• 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_1447
AATCGTTATGATGACCCAGGCAGCAGAGACTATGACAGAGGCTATGGTTCCAGGATAGACAGTGGCAGAAGAGCATTTGG
TAGTGGGTACCGTAGGGATGATGACTACAGAGGAGGCAGGGACCGCTATGAAGATAGATATGACAGACCAGATGACCAGG
GATGGAGCTCCAGTGATGATTACTCTCGGGATGACTATAGGCGTGATGATAGAGGTCCCCCTCCCAAAAAAAGACCCAAA
CTGAATCTAAAGCCTCGGAGTACTCCTAAGGAAGATGGTTCCTCTGCTAGCACCTCCCAATCCAGTTGAGAGGCCTCTGT
CTTTGGAGGGGCAAAGCCTGTTGACACAGCTGCTAGAGAGCAAGAAGTAGAAGAGCAGCTGCAGAAGGAGCAGGAGAAGC
TGCAGCGCCAGCTGGATGAGCCAAACAAAACTAGAGTGACGGCCTCGAGAGAGACACCCAAGCTGGAGAAAGTGAAGAGA
CTCAGGGATGGTAATGGTCCAGGACAGGAGGTGAGTCATCACAGACTGGGACCTCGGCCACATCTGGCAGAAATGCACGA
AGGAGAGAGAGTGAGAAGTGTCTAGAAAATGAAACACCCAATAAGGAGGAAGACTGTCACTCTCCAACTTCTAAGCCACC
CAAATCTGAACAGCCTCTGAAGGTAATGCCAGCCCCTCCACCAAAGGAGTATGCTTGGATGAAGCGAAGTTCTAACCCTC
TTGCTCCATCTCAGAGCTCAGACACAGAGCAGCAGTCCCCTACAGGTGGTGGGGGGAAAGCAGTCCCAGCCTAATCACAG
GAGGGAGGACCAGCAAGGAGAGCAGATGAAAACAAAGTAGATGGGGTGAGTGTCCCAAAAGGCCCCAGTGGGAACTCCAG
CCGTGGTCCAGGAGATGGAGGGAACAAAGACCACTGGAAGGAGCCAGATTGGAAAGACGGTAAAAAGGATCAAGACTCCC
GATCTACACCTAATTAAAAGAAACCTGAAGAAAATCCAGCTTCCAAGTTCAGTTCTGCAAGCAAGTATGCTGCTCTCTCC
ATTGATGGTGAAGATGAGAACAAAGGAGAAGATTACACCGAA

Alignment

ORF - retro_cfam_1447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.9 %
• Parental protein coverage: 58.33 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DRYDDRGSRDYDRGYDSRIGSGRRAFGSGYRRDDDYRGGGDRYEDRYDRRDDRSWSSRDDYSRDDYRRDD
          .RYDD.GSRDYDRGY.SRI.SGRRAFGSGYRRDDDYRGG.DRYEDRYDR.DD..WSS.DDYSRDDYRRDD
Retrocopy NRYDDPGSRDYDRGYGSRIDSGRRAFGSGYRRDDDYRGGRDRYEDRYDRPDDQGWSSSDDYSRDDYRRDD

Parental  RGPP--QRPKLNLKPRSTPKEDDSS-ASTSQSSRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQ-L
          RGPP...RPKLNLKPRSTPKED.SS......S..A....G.......A......E...............
Retrocopy RGPPPKKRPKLNLKPRSTPKEDGSSASTSQSS*EASVFGGAKPVDTAAREQEVEEQLQKEQEKLQRQL>M

Parental  DEPKLERRPRERHPSWR-SEETQERERSRTGSESSQTGTSATTGRNARRRESEKSLENETPNKEEDCHSP
          ...KLE.RPRERHPSWR.SEETQ....SRTG.ESSQTGTSAT.GRNARRRESEK.LENETPNKEEDCHSP
Retrocopy SQTKLE*RPRERHPSWR>SEETQGW*WSRTGGESSQTGTSATSGRNARRRESEKCLENETPNKEEDCHSP

Parental  TSKPPKSEQPLKVMPAPPPKENAWVKRSSNPPARSQSSDTEQQSPTSGGGKAVPAQPPEEGPARRADENK
          TSKPPKSEQPLKVMPAPPPKE.AW.KRSSNP.A.SQSSDTEQQSPT.GGGKAVPA...E.GPARRADENK
Retrocopy TSKPPKSEQPLKVMPAPPPKEYAWMKRSSNPLAPSQSSDTEQQSPTGGGGKAVPA*SQEGGPARRADENK

Parental  VDGVSVPKGHSGNSSRGPGDGGNKDHWKEPDRKDGKKDQDSRSAPEPKKPEENPASKFSSASKYAALSID
          VDGVSVPKG.SGNSSRGPGDGGNKDHWKEPD.KDGKKDQDSRS.P..KKPEENPASKFSSASKYAALSID
Retrocopy VDGVSVPKGPSGNSSRGPGDGGNKDHWKEPDWKDGKKDQDSRSTPN*KKPEENPASKFSSASKYAALSID

Parental  GEDENEGEDYTE
          GEDEN.GEDYTE
Retrocopy GEDENKGEDYTE

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	226.16 RPM
SRP017611_brain	0.16 RPM	109.32 RPM
SRP017611_kidney	0.00 RPM	443.97 RPM
SRP017611_liver	0.00 RPM	426.02 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1447 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1447 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1447 has 0 orthologous retrocopies within eutheria group .

---

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,