RetrogeneDB ID: retro_rnor_2972

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:117876147..117877121(-)
• 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_2972
ATGGTGGCCTCAGCAAAAAAGAAGAATAAGAAGAGGAAGACCATCTCCCTAACAGACTTTCTAGCTGAGGATGGGGGAAC
TGGTGGAGGAAGCACCTATATCCCCAAACCAGTTAGCTTGGCTGATGAAACAGACGATCTGGAAGGAGATGGGTCAACAA
CTTGGCATAGTAACGATGACGATGTGTACAGGGCACCTCCTATTGACCGTTCCATCCTTCCCACTGCTCCACGGGCTTCT
CAGGAACCCAATATTGATCGGAGCCATCTTCCCAAGTCACCACCCTACACTGCTTTCCTAGGGAATCTGCCCTCTGATGT
GACAGAAGACTCCATTAAGGATTTCTTTAGAGGATTAAATATCAGCGCTGTACGCTTACCACGTGAACCCAGCACTCTAG
ACAGGTTGAAAGGTTTTGGCTATGCGGAATTTGAGGATCTGGATTCTCTGCTCTGATTCTCAATGAAAAGTCTCTAGGTA
ACAGGAGAATTCGGGTGGATGTTGCTGATCAAGCACAGGATAATGACAGGGATGACCGTTCTTTTGGTCAAGATAGAAAT
CAGGATTCTGACAAGATAGACACAGACTGGAGGGCCCGTCCTGTCACAAACAGCTTTGATGACTACCCACCTAGACGAGG
TGATGACAGCTTCGGAGACAAGTATCAAGATCGTTACGACTCAGACCGGTATCCGGATGGGTATAGGGACGGATATCGGG
ATGGCCCATGCAGAGACATGGACCGCTATGGGGGCCGGGATCGCTATGATGACCGAGGCAGCAGAGACTATGACCTAGGC
TATGACTCCAGGATAGGCAGTGGTAGAAGAGCATTTGGAAGTGGGTACCGGAGGGATGATGACTACAGAGGAGGTGGGGA
CCGCTATGAAGACTGCTATGACAGACGGGAGGATCGGTCATGGAGCTCCAGGGACGATTATCACTCTTGGGACGATTACA
GGCGTGATGACAGA

Alignment

ORF - retro_rnor_2972 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.11 %
• Parental protein coverage: 53.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVPKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDR
          M.ASAKKKNKK.KTISLTDFLAEDGGTGGGSTY.PKPVS.ADETDDLEGD.STTWHSNDDDVYRAPPIDR
Retrocopy MVASAKKKNKKRKTISLTDFLAEDGGTGGGSTYIPKPVSLADETDDLEGDGSTTWHSNDDDVYRAPPIDR

Parental  SILPTAPRAAREPNIDRSRLPKSPPYTAFLGNLPYDVTEDSIKDFFRGLNISAVRLPREPSNPDRLKGFG
          SILPTAPRA..EPNIDRS.LPKSPPYTAFLGNLP.DVTEDSIKDFFRGLNISAVRLPREPS..DRLK..G
Retrocopy SILPTAPRASQEPNIDRSHLPKSPPYTAFLGNLPSDVTEDSIKDFFRGLNISAVRLPREPSTLDRLK--G

Parental  YAEFEDLD-SLLSALSLNEESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPATDSFD
          ....E..D.S..SAL.LNE.SLGNRRIRVDVADQAQD.DRDDRSFG.DRN.DSDK.DTDWRARP.T.SFD
Retrocopy FGYAEFED<SGFSALILNEKSLGNRRIRVDVADQAQDNDRDDRSFGQDRNQDSDKIDTDWRARPVTNSFD

Parental  DYPPRRGDDSFGDKYRDRYESDRYRDGYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGRR
          DYPPRRGDDSFGDKY.DRY.SDRY.DGYRDGYRDGP.RDMDRYGGRDRYDDRGSRDYD.GYDSRIGSGRR
Retrocopy DYPPRRGDDSFGDKYQDRYDSDRYPDGYRDGYRDGPCRDMDRYGGRDRYDDRGSRDYDLGYDSRIGSGRR

Parental  AFGSGYRRDDDYRGGGDRYEDRYDRRDDRSWSSRDDY-SRDDYRRDDR
          AFGSGYRRDDDYRGGGDRYED.YDRR.DRSWSSRDDY.S.DDYRRDDR
Retrocopy AFGSGYRRDDDYRGGGDRYEDCYDRREDRSWSSRDDYHSWDDYRRDDR

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	0.14 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_2972 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2972 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2972 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,