RetrogeneDB ID: retro_pabe_3169

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:106345617..106346572(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3I
• Ensembl ID: ENSPPYG00000001598
• Aliases: EIF3I, EIF3S2, eIF-3-beta
• Description: eukaryotic translation initiation factor 3 subunit I [Source:RefSeq peptide;Acc:NP_001126286]

Sequence

>retro_pabe_3169
ATGAAGCTGGTCCTACTGAAGGGCCATGAGTGGTTCATTAGGCAGATGAAGTATAACTGTGAAGGAGACCTCCTCTTCAC
CGTGGCCAAGGAACCTATCATTAATGCATGGTACTCTGTGAATGGTGAGAGGCTGGGCATCTACATGGACCATACCAGAG
CTGTGTGGTATGTGGACGCTGACTGGGACACCAAGCATGTCCTCACCCGTTCAGCTGACAACCATCTTTGGGCCTGTGAA
ACAGGGAAACAGCTGGTCCTACTCAAGACCAATTCAACTGTATGGATCTGCAGTTTTGACTTTGGGGGCAATATCATCAC
TTTCTCCACGGAGAAGCAGAAAAGCTATCAGTGCTTTGTGAGCTTATTTGACCTGCAGGATCTGAGCCAGATTGACAGCA
ATGAGTGCCACCTAAAGATCCCTTGCAATGACTCTAAAATCACTAGTGCCGTTTGGGGCTCCTGTGGGGAGTGCATCATT
GCATGCCATGACAGTGGAAAGCTCAACCAGTATAGTGCCAAGCCTGGGGAGGTGTTGGTGAATGTTAAGGAGCACTCCCA
GCAGATTAATGACATCCAGTTATCCAGGGACATGACCGTGTTTGTCACTGCATCCAAAGACAACACAGCCAAGCTTTTTG
ACTCTACAACTCTTCAACATCAGAAGACTTTCTGAACAGAAAGCCCCATCAGCTCAGCTACCCTCTTCCCCAGCTATGAC
CATATTTTGCTGGGCAGTGGTCAGGAAGCCATGGATGTAACCACAACCTTCACCAGGATTGGCAAGTTTGAGTCTGGGTT
CCTCCATTTGGCCTTCGAAGAAGAGTTCAGAAGAGTCAAGGGGCACTTTGGACATATCAACAGTGTTGCCTTCTATCCTG
ATGGCAAGAGCTACAGCAGTGGCAGTGGGGATGGTTACATCCATAATCTACTACTTCGACCCACAGTACTTTGAA

Alignment

ORF - retro_pabe_3169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.82 %
• Parental protein coverage: 98.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKPILLQGHERSITQIKYNREGDLLFTVAKDPIVNVWYSVNGERLGTYMGHTGAVWCVDADWDTKHVLTG
          MK..LL.GHE..I.Q.KYN.EGDLLFTVAK.PI.N.WYSVNGERLG.YM.HT.AVW.VDADWDTKHVLT.
Retrocopy MKLVLLKGHEWFIRQMKYNCEGDLLFTVAKEPIINAWYSVNGERLGIYMDHTRAVWYVDADWDTKHVLTR

Parental  SADNSCRLWDCETGKQLALLKTNSAVRTCGFDFGGNIIMFSTDKQMGYQCFVSFFDLRDPSQIDNNEPYM
          SADN...LW.CETGKQL.LLKTNS.V..C.FDFGGNII.FST.KQ..YQCFVS.FDL.D.SQID.NE...
Retrocopy SADN--HLWACETGKQLVLLKTNSTVWICSFDFGGNIITFSTEKQKSYQCFVSLFDLQDLSQIDSNECHL

Parental  KIPCNDSKITSAVWGPLGECIIAGHESGELNQYSAKSGEVLVNVKEHSRQINDIQLSRDMTMFVTASKDN
          KIPCNDSKITSAVWG..GECIIA.H.SG.LNQYSAK.GEVLVNVKEHS.QINDIQLSRDMT.FVTASKDN
Retrocopy KIPCNDSKITSAVWGSCGECIIACHDSGKLNQYSAKPGEVLVNVKEHSQQINDIQLSRDMTVFVTASKDN

Parental  TAKLFDSTTLEHQKTFRTERPVNSAALSPNYDHVVLGGGQEAMDVTTTSTRIGKFEARFFHLAFEEEFGR
          TAKLFDSTTL.HQKTF.TE.P..SA.L.P.YDH..LG.GQEAMDVTTT.TRIGKFE..F.HLAFEEEF.R
Retrocopy TAKLFDSTTLQHQKTF*TESPISSATLFPSYDHILLGSGQEAMDVTTTFTRIGKFESGFLHLAFEEEFRR

Parental  VKGHFGPINSVAFHPDGKSYSSGGEDGYVR-IHYFDPQYFE
          VKGHFG.INSVAF.PDGKSYSSG..DGY...I.YFDPQYFE
Retrocopy VKGHFGHINSVAFYPDGKSYSSGSGDGYIH>IYYFDPQYFE

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_prefrontal_cortex	0.00 RPM	48.10 RPM
SRP007412_cerebellum	0.00 RPM	36.24 RPM
SRP007412_heart	0.00 RPM	29.92 RPM
SRP007412_kidney	0.00 RPM	65.53 RPM
SRP007412_liver	0.00 RPM	52.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3169 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3169 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3169 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3888
Gorilla gorilla	retro_ggor_2615

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010674	1 retrocopy	retro_cfam_321,
Callithrix jacchus	ENSCJAG00000006810	1 retrocopy	retro_cjac_3104,
Echinops telfairi	ENSETEG00000008047	1 retrocopy	retro_etel_1497,
Homo sapiens	ENSG00000084623	2 retrocopies	retro_hsap_3888, retro_hsap_3894,
Gorilla gorilla	ENSGGOG00000001579	3 retrocopies	retro_ggor_2540, retro_ggor_2615, retro_ggor_2623,
Loxodonta africana	ENSLAFG00000017026	1 retrocopy	retro_lafr_1073,
Macaca mulatta	ENSMMUG00000006119	2 retrocopies	retro_mmul_1730, retro_mmul_1733,
Monodelphis domestica	ENSMODG00000017481	2 retrocopies	retro_mdom_1054, retro_mdom_822,
Nomascus leucogenys	ENSNLEG00000002426	2 retrocopies	retro_nleu_1129, retro_nleu_1135,
Pongo abelii	ENSPPYG00000001598	2 retrocopies	retro_pabe_3169 , retro_pabe_3175,
Pongo abelii	ENSPPYG00000004334	3 retrocopies	retro_pabe_2005, retro_pabe_3134, retro_pabe_3212,