RetrogeneDB ID: retro_rnor_2467

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:86665081..86666015(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif4b
• Ensembl ID: ENSRNOG00000010103
• Aliases: None
• Description: eukaryotic translation initiation factor 4B [Source:RefSeq peptide;Acc:NP_001008325]

Sequence

>retro_rnor_2467
AAATCCAATAAAAAAGAAGATTCAGACTGGTATAAGGCTGGTTATAGGGTCCATTATTCGGATGGCCCGTACAGAGACAT
GAACCGCTATGGGATCCAGAATCGCTATGATGACCTAAGCAGCAGAGCCTACGACCAAAGCTATGACTCCAGGATAGGCA
GTGGCAGAAAAGCATTTGGAAGTGTTTACTGGAGGGATGATGACTACAGAGGAAGTGGGGACCGTTTTGAAGATCTATAT
GACAGAAGGGATGATCTGTCATAGAGGTCCAGGGATGATTACTCTAAGGATGATTATAGGTGTGATGACAGAGCCTCCCT
TCCCCTCCCTCCCTGCCAAAGACCCAAACTGAATCGAAAGCCTCGCAGTACTCCTAAAGAAGATTCCTCTGCTCCTCTGC
CTGCACCTCCTAGTCGGGCCGAGTGCCTTCTATCTTGACACAGCTACTATAGAAAGAGCTGCTAGAGCAGCGGCTACAGA
AAGAGGAGGAGGAGAAGCTGCAGCGTCAGCTGGATGAACCAAAACTAGACCACCCACTCCCTGGAAAGACACCCAAATTG
GTGAAGCGTAGAAATTCAGGAAGAAAATGGTAGAGGACAGGAAGTGAGTCATTGTAGACTGGCACCTAAGCCACATCTGG
CAGAAGTCAAACCGGGATAGGAAGGAATGAGAGTGAGAATTTTCTAGAAAATGAAACCCTCAATAAAGAAGACTGACACT
CTCCCACATTTAAGCCTCCTAAACCTGATAGTCTCTAAAGATAATCTCAACCCCTCCACCAAAGGAGAATGCGTGGTTGA
ACCAAAGCTCGTACCCTCCTGCTCTATCTCATAGCTCAGACACAGAGCAGCAGTGCCCTACACGTGGTGGAGGGAAAGTA
GCTCCAGTTCAACCATCTGTGGAAGGACCATGAAGGAAAGATGAAAATAAAGTA

Alignment

ORF - retro_rnor_2467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.37 %
• Parental protein coverage: 50.41 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KYRDRYESDRYRDGYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRAFGSGYRRDDDYR
          K......SD.Y..GYR..Y.DGP.RDM.RYG...RYDD..SR.YD..YDSRIGSGR.AFGS.Y.RDDDYR
Retrocopy KSNKKEDSDWYKAGYRVHYSDGPYRDMNRYGIQNRYDDLSSRAYDQSYDSRIGSGRKAFGSVYWRDDDYR

Parental  GGGDRYEDRYDRRDDRSWSSRDDYSRDDYRRDDRG----PP-QRPKLNLKPRSTPKEDDSSASTSQSSRA
          G.GDR.ED.YDRRDD.S..SRDDYS.DDYR.DDR.....PP.QRPKLN.KPRSTPKED.S.......SRA
Retrocopy GSGDRFEDLYDRRDDLS*RSRDDYSKDDYRCDDRASLPLPPCQRPKLNRKPRSTPKEDSSAPLPAPPSRA

Parental  -ASIFGGAKPVDTAAR-EREVEERLQKEQEKLQRQLDEPKLDR-RPRERHPSWRSEETQE-RERSRTGSE
          .............AAR..R...E...K.Q..L....DEPKLD.....ERHP.W.S.E.QE.R...RTGSE
Retrocopy >SAFYLDTATIERAAR>QRLQKEEEEKLQRQL----DEPKLDH>HSLERHPNW*SVEIQE<RKW*RTGSE

Parental  SSQTGTSATSGRNTR---RRESEKSLENETLNKEEDCHSPTSKPPKPDQ-PLKVMPAPPPKENAWVKRSS
          S..TGT.ATSGR......R.ESE..LENETLNK.ED.HSPT.KPPKPD...LK....PPPKENAW...SS
Retrocopy SL*TGT*ATSGRSQTGIGRNESENFLENETLNK-ED*HSPTFKPPKPDS<SLKIISTPPPKENAWLNQSS

Parental  NPPARSQSSDTEQPSPTSGGGKVAPAQPSEEGPSRKDETKV
          .PPA.S.SSDTEQ..PT.GGGKVAP.QPS.EGP.RKDE.KV
Retrocopy YPPALSHSSDTEQQCPTRGGGKVAPVQPSVEGP*RKDENKV

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
SRP017611_brain	0.00 RPM	176.15 RPM
SRP017611_kidney	0.00 RPM	258.40 RPM
SRP017611_liver	0.00 RPM	122.51 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2467 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2467 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2467 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 49 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,
Callithrix jacchus	ENSCJAG00000018176	2 retrocopies	retro_cjac_1717, retro_cjac_2001,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937,
Homo sapiens	ENSG00000063046	7 retrocopies	retro_hsap_1686, retro_hsap_2639, retro_hsap_2698, retro_hsap_3767, retro_hsap_4196, retro_hsap_4848, retro_hsap_4891,
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,
Nomascus leucogenys	ENSNLEG00000017727	3 retrocopies	retro_nleu_2371, retro_nleu_2601, retro_nleu_721,
Pongo abelii	ENSPPYG00000025848	7 retrocopies	retro_pabe_1388, retro_pabe_1560, retro_pabe_2283, retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Rattus norvegicus	ENSRNOG00000001454	1 retrocopy	retro_rnor_2924,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467 , retro_rnor_2972,
Ictidomys tridecemlineatus	ENSSTOG00000006800	1 retrocopy	retro_itri_604,
Tupaia belangeri	ENSTBEG00000005423	2 retrocopies	retro_tbel_2363, retro_tbel_4167,
Tarsius syrichta	ENSTSYG00000012880	1 retrocopy	retro_tsyr_452,