RetrogeneDB ID: retro_cfam_1127

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 23:42839378..42840618(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3E
• Ensembl ID: ENSCAFG00000000702
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit E [Source:HGNC Symbol;Acc:3277]

Sequence

>retro_cfam_1127
GAGATATATAATGAAAAAGAATTATTACAAGGGGAATTAGACCTTCTTCTTCATGATACCAATGTGGTAGGCTTTGTGGG
TGATGTATACAAAACCTTTATTCTGATGATATTCCATTTGTTTTGAGAGAAAAAAAGAACCTCAGCTGTTGCACAACTGA
AACAGCTTCAGGCAGAAACGGGACCAGTCATGATAATGTTTGATCCAGAAACTACAAGGAAGATGCTGTCAACCAGAGAT
GGTCAGATGTTGGTTGACTCACTGGAGGACAAGCATGATTTTAGGCAGGAATGTTTAGATACATCTCACAGGTATGAAAA
ATTCCAATATGAATGTGGGCATTGGGCATTACCCTGGAATGTCTTTACTTCTTTAGAGTGTTGGTTCCAGCAGCAGATAG
AAGTGCTTTGAGTTCACTCTGGGAAAACTGGCCTCTGAGATCTTAATGTGGAATTGGGATGCCTCCATGGAAGACCTGAC
AGGGTTAAAAGAAACCACAGAAGTAATTCTGTGAGCTCTCCCTTTCAGCCTCTTCGGCAGCAAACATGGCTCATCCACTG
GTCTTGGTTTGTTTTCTTCACCCACCCCAAAGGGCGTGATAACTTTATTGATCTCTTCCTTTACCAGCCACAGTGTCTTG
ATGTAATTCAGATGATGTGTCCACTTATTCTGCACCATTTGACTACACCCACCATAACAAACAAAACATCTGAAAACCCC
AACAGGTGTTAAAAGATTCCGTTAAAGTTATTCAACAGGAGTCTTACACATAGAAAGACCCAGTGACAAAATTAGTTGAA
TGTTTATCTGTTAACTTTGGCTTCAGTAGGGCTCAGGAAAAGCTGAGGGACTGTGAATCAGTACTTATGAATGACTTCTT
GGTGGCTTGTTTTGAAGATTTCACTGAAAATGCACCTCTCATCACACTTGAGACTTTTTATTCACCCACCAGTGTATCAA
CATTAACATGTTGGCAGACAAACTAAACATGATTCCAGAAGAAGCTGAAAGGTGGCTTATAAATGTGATCATCAATGCAA
GACTGGGTGCCAAGATTGATTCTAAATTAGGTCTTGTGGTTATGGGTAACAAAACAATCTCACCCTATCAGCAAGTGATT
GAAAAGACCAGAAGCCTTTCATTTAGAAGCCAGATGTTTGCCATGAATATTGAGAATAAACTTAATCAGAATAGTAGGTC
AGAAGCTCCTAACTGGGCAGCTCAGGATTCTGGCTTCTAC

Alignment

ORF - retro_cfam_1127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.76 %
• Parental protein coverage: 93.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  EIYNEKELLQGKLDLL-SDTNMVDFAMDVYK-NLYSDDIPHALREK-RTTVVAQLKQLQAETEPIVKMFE
          EIYNEKELLQG.LDLL..DTN.V.F..DVYK.NLYSDDIP..LREK.RT..VAQLKQLQAET.P...MF.
Retrocopy EIYNEKELLQGELDLLLHDTNVVGFVGDVYK<NLYSDDIPFVLREK>RTSAVAQLKQLQAETGPVMIMF-

Parental  DPETTRQMQSTRDGRMLFDYLADKHGFRQEYLDTLYRYAKFQYECGNYSG-AAEYLYFFRVLVPATDRNA
          DPETTR.M.STRDG.ML.D.L.DKH.FRQE.LDT..RY.KFQYECG.......E.LYFFRVLVPA.DR.A
Retrocopy DPETTRKMLSTRDGQMLVDSLEDKHDFRQECLDTSHRYEKFQYECGHWAL<TLECLYFFRVLVPAADRSA

Parental  LSSLW-GKLASEILMQNWDAAMEDLTRLKETID-NNSVSSPLQSLQQRTWLIHWSLFVFFNHPKGRDNII
          LSSLW.GKLASEILM.NWDA.MEDLT.LKET....NSVSSP.Q.L.Q.TWLIHWS.FVFF.HPKGRDN.I
Retrocopy LSSLW<GKLASEILMWNWDASMEDLTGLKETTE<SNSVSSPFQPLRQQTWLIHWSWFVFFTHPKGRDNFI

Parental  DLFLYQPQYLNAIQTMCPHILRYLTTAVITNK-DVRKRRQVLKDLVKVIQQESYTYKDPITEFVECLYVN
          DLFLYQPQ.L..IQ.MCP.IL..LTT..ITNK....K..QVLKD.VKVIQQESYT.KDP.T..VECL.VN
Retrocopy DLFLYQPQCLDVIQMMCPLILHHLTTPTITNK<NI*KPQQVLKDSVKVIQQESYT*KDPVTKLVECLSVN

Parental  FDFDGAQKKLRECESVLVNDFFLVACLEDFIENARLFIFETFCR-IHQCISINMLADKLNMTPEEAERWI
          F.F..AQ.KLR.CESVL.NDF.LVAC.EDF.ENA.L...ETF....HQCI.INMLADKLNM.PEEAERW.
Retrocopy FGFSRAQEKLRDCESVLMNDF-LVACFEDFTENAPLITLETFYS<THQCININMLADKLNMIPEEAERWL

Parental  VNLIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRSQMLAMNIEKKLNQNSRSEAPNWATQD
          .N.I.NARL.AKIDSKLG.VVMGN...SPYQQVIEKT.SLSFRSQM.AMNIE.KLNQNSRSEAPNWA.QD
Retrocopy INVIINARLGAKIDSKLGLVVMGNKTISPYQQVIEKTRSLSFRSQMFAMNIENKLNQNSRSEAPNWAAQD

Parental  SGFY
          SGFY
Retrocopy SGFY

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	0.08 RPM	122.80 RPM
SRP017611_brain	0.00 RPM	40.57 RPM
SRP017611_kidney	0.00 RPM	262.04 RPM
SRP017611_liver	0.00 RPM	85.42 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1127 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1127 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1127 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006702	1 retrocopy	retro_btau_291,
Canis familiaris	ENSCAFG00000000702	1 retrocopy	retro_cfam_1127 ,
Callithrix jacchus	ENSCJAG00000006458	3 retrocopies	retro_cjac_2333, retro_cjac_2686, retro_cjac_701,
Equus caballus	ENSECAG00000000236	1 retrocopy	retro_ecab_860,
Echinops telfairi	ENSETEG00000013105	1 retrocopy	retro_etel_2048,
Felis catus	ENSFCAG00000003665	1 retrocopy	retro_fcat_231,
Homo sapiens	ENSG00000104408	1 retrocopy	retro_hsap_3489,
Gorilla gorilla	ENSGGOG00000022955	2 retrocopies	retro_ggor_2354, retro_ggor_2355,
Myotis lucifugus	ENSMLUG00000007269	1 retrocopy	retro_mluc_1796,
Macaca mulatta	ENSMMUG00000011359	1 retrocopy	retro_mmul_2585,
Mustela putorius furo	ENSMPUG00000005924	2 retrocopies	retro_mputfur_193, retro_mputfur_736,
Mus musculus	ENSMUSG00000022336	2 retrocopies	retro_mmus_1801, retro_mmus_2807,
Nomascus leucogenys	ENSNLEG00000004120	1 retrocopy	retro_nleu_333,
Oryctolagus cuniculus	ENSOCUG00000008050	1 retrocopy	retro_ocun_1399,
Pan troglodytes	ENSPTRG00000020505	1 retrocopy	retro_ptro_2362,
Rattus norvegicus	ENSRNOG00000027690	4 retrocopies	retro_rnor_1133, retro_rnor_2879, retro_rnor_583, retro_rnor_584,
Ictidomys tridecemlineatus	ENSSTOG00000008976	1 retrocopy	retro_itri_545,
Tursiops truncatus	ENSTTRG00000011025	2 retrocopies	retro_ttru_1602, retro_ttru_1794,