RetrogeneDB ID: retro_mmul_783

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:7539792..7541007(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.9577
• Ensembl ID: ENSMMUG00000001062
• Aliases: None
• Description: eukaryotic translation initiation factor 4B [Source:RefSeq peptide;Acc:NP_001182737]

Sequence

>retro_mmul_783
AAAAAGAAGAAGAAGGGGAAGACTATCTCCCTAACAGACTTTCTGGCTGAGGATGGGGGTACTGGTGGAGGAAGCACCTA
TGTTTCCAAACCAGTCAGCTGGGCTGATGAAACGGATGATCTGGAAGGAGATGTTTCAACAACGTGGCACAGTAATGACG
ACGATGTGTACAGGGCGCCTCCAATTGACCGTTCCATCCTTCCCACTGCTCCACGGGCTGCTCGGGAACCCAATATCGAC
CGGAGCCGTCTTCCCAAATCGCCACCCTACACTGCTTTTCTAGGGAAGCTACCCTATGATGTGACAGAAGAGTCAATTAA
GGAATTCTTTAGAGGATTAAATATCAGTGCAGTGCGTTTACCACGTGAACCCAGCAATCCAGAGAGGTTGAAAGGTTTTG
GTTATGCTGAATTTGAGGACCTGGATTCCCTGCTCAGTCCCCTGAGTCTCAATGAAGAGTCTCTAGGTAACAGGAGAATT
CGAGTGGACGTTGCTGATCAAGCACAGGATAAAGACAGGGATGATCGTTCTTTTGGCCGTGATAGAAATCGGGATTCTGA
CAAAACAGATACAGACTGGAGGGCTCGTCCTGCTACAGACAGCTTTGATGGCTACCCACCTAGAAGAGGTGATGATAGCT
TTGGAGACACGTATCGAGATCGTTATGATTCAGACTGGTATCGGGATGGGTATCGGGATGGCCCACGCCGGGATATGGAT
CGATATGGTGGCCAGGATCGCTATGATGACCGAGGCAGCAGAGACTATGACAGAGGCTATGATTCCCGGATAGGCAGTGG
CAGAAGAGCATTTGGCAGTGGGTATCGCAGGGATGATGACTACAGAGGAGGCGGGGACCGCTATGAAGACGGATACCACA
GACGGGATGATCGGTCGTGGAGCTCCAGAGATGATTACTCTCGGGATGATTATAGGCGCGATGACAGAGGTCCCCCTCAA
AGACCCAAACTGAATCTAAAGCCTCGGAGTACTCCTAAGGAAGATGATTCCTCTGCTAGTACCTCCCAGTCCAGTCGAGC
TGCTTCTATCTTTGGAGGGGCAAAGCCTGTTGACACAGCTGCTAGAGAAAGAGAAGTAGAAGAACTGCTACAGAAGGAAC
AAGAGAAGTTGCAGCATCAGCTGGATGAGCCAAAACTAGAACGACGGCCTCGGGAGAGACACCCAAGCTGGCGAAGTGAA
GAAACTCAGGAACGG

Alignment

ORF - retro_mmul_783 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.06 %
• Parental protein coverage: 66.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDRSILPTA
          KK.KKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDRSILPTA
Retrocopy KKKKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDRSILPTA

Parental  PRAAREPNIDRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFED
          PRAAREPNIDRSRLPKSPPYTAFLG.LPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFED
Retrocopy PRAAREPNIDRSRLPKSPPYTAFLGKLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFED

Parental  LDSLLSALSLNEESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPATDSFDDYPPRRG
          LDSLLS.LSLNEESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPATDSFD.YPPRRG
Retrocopy LDSLLSPLSLNEESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPATDSFDGYPPRRG

Parental  DDSFGDKYRDRYDSDRYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYESRIGSGRRAFGSGYRRDDD
          DDSFGD.YRDRYDSD.........PRRDMDRYGG.DRYDDRGSRDYDRGY.SRIGSGRRAFGSGYRRDDD
Retrocopy DDSFGDTYRDRYDSDXXXXXXXXXPRRDMDRYGGQDRYDDRGSRDYDRGYDSRIGSGRRAFGSGYRRDDD

Parental  YRGGGDRYEDRYDRRDDRSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSASTSQSSRAASI
          YRGGGDRYED.Y.RRDDRSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSASTSQSSRAASI
Retrocopy YRGGGDRYEDGYHRRDDRSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSASTSQSSRAASI

Parental  FGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPRERHPSWRSEETQER
          FGGAKPVDTAAREREVEE.LQKEQEKLQ.QLDEPKLERRPRERHPSWRSEETQER
Retrocopy FGGAKPVDTAAREREVEELLQKEQEKLQHQLDEPKLERRPRERHPSWRSEETQER

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
SRP007412_brain	0.22 RPM	42.80 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	92.18 RPM
SRP007412_cerebellum	0.32 RPM	45.72 RPM
SRP007412_heart	0.29 RPM	75.55 RPM
SRP007412_kidney	0.23 RPM	50.47 RPM
SRP007412_liver	0.04 RPM	43.46 RPM
SRP007412_testis	0.23 RPM	80.06 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_783 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_783 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_783 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 50 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 ,
Macaca mulatta	ENSMMUG00000006205	2 retrocopies	retro_mmul_2634, retro_mmul_619,
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	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,