RetrogeneDB ID: retro_ptro_940

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:81284316..81285134(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3L
• Ensembl ID: ENSPTRG00000014352
• Aliases: EIF3L, EIF3EIP, EIF3S6IP
• Description: Pan troglodytes eukaryotic translation initiation factor 3, subunit L (EIF3L), mRNA. [Source:RefSeq mRNA;Acc:NM_001135207]

Sequence

>retro_ptro_940
ATGTCTTATCTCGCGATGATTATGAGTCTGAGGAGGCTTATGACCCCTATACTTATCTGGGCGACTATGGAGATCCAAAA
GCAGGGCCTTGCTTATGAACGTCAGTATGAATAGCAAACCTATCAGGTAATGCCTGAAGTGATCAAAAACTCCATCTAGT
ATTTACACAAAACTGTCTCGGATTTGACTGACCAGAAAGCGTATGAGCTACAGGCCAGTTGTGTCTCTAGTGATGTCATT
GACCAGAAGGTGTATAGGATCCAGGACATCTATGAGAACAGCTGGACCAAGCTGACTGAAAGATTCTTCAAAACTACACC
TTGGCCCGAGGCTGAAGCCATTGCTCCACAGGTTGGCAACAATGCTGTCTTCCTGGTTTTATATAAAGAATTATACTACA
GGCACATATATGCCAAAGTCAGTGGGGGACCTTCCTTGGAGCAGAGGTTTGAATCCTATTATAACAATTGCAATCTCTTC
AACTATATTCTTAATGTTGATGGTCCTCCTTCCCTTGAACTACCCAACCAGGGGCTCTAGGATATCATTGATGAGTTCAT
CTACCAGTTTCAGTCATTCAGTCAGTACTGCTGTAAGACTGCTAAGAAGTCGGAGGAGGAGATTGACTTCCTTTGTTCCA
ATCCCAAAATCTGGATTGTTCACAGTGTCCTCAATGTCCTTCATTCCTGGGTAGACAAATCCAACATCAACTGACAGTTG
GAGGTATACACAAGCGAGGTGACCCTGACAGTGTGGCTGGGGAGATGCTTGGTTACTTCAGCCTCGTGGGGTTTCTCTGC
CTGCACTCCCTGTTAGGA

Alignment

ORF - retro_ptro_940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.5 %
• Parental protein coverage: 76.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSYPA-DDYESEAAYDPYAYPSDYDMHTGDPK-QDLAYERQYEQQTYQVIPEVIKNFIQYFHKTVSDLID
          MSY.A.DDYESE.AYDPY.Y..DY....GDPK.Q.LAYERQYE.QTYQV.PEVIKN.I.Y.HKTVSDL.D
Retrocopy MSYLA<DDYESEEAYDPYTYLGDY----GDPK>QGLAYERQYE*QTYQVMPEVIKNSI*YLHKTVSDLTD

Parental  QKVYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLILYKELYYR
          QK.YELQAS.VSSDVIDQKVY.IQDIYENSWTKLTERFFK.TPWPEAEAIAPQVGN.AVFL.LYKELYYR
Retrocopy QKAYELQASCVSSDVIDQKVYRIQDIYENSWTKLTERFFKTTPWPEAEAIAPQVGNNAVFLVLYKELYYR

Parental  HIYAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPNQWLWDIIDEFIYQFQSFSQYRCKTAKKS
          HIYAKVSGGPSLEQRFESYYN.CNLFNYILN.DGP..LELPNQ.L.DIIDEFIYQFQSFSQY.CKTAKKS
Retrocopy HIYAKVSGGPSLEQRFESYYNNCNLFNYILNVDGPPSLELPNQGL*DIIDEFIYQFQSFSQYCCKTAKKS

Parental  EEEIDFLRSNPKIWNVHSVLNVLHSLVDKSNINRQLEVYTS-GGDPESVAGE-YGRHSLYKMLGYFSLVG
          EEEIDFL.SNPKIW.VHSVLNVLHS.VDKSNIN.QLEVYTS..GDP.SVAGE..G..SL...L...SL.G
Retrocopy EEEIDFLCSNPKIWIVHSVLNVLHSWVDKSNIN*QLEVYTS<RGDPDSVAGEMLGYFSLVGFLCLHSLLG

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	41.68 RPM
SRP007412_cerebellum	0.00 RPM	94.35 RPM
SRP007412_heart	0.00 RPM	53.40 RPM
SRP007412_kidney	0.03 RPM	102.85 RPM
SRP007412_liver	0.00 RPM	45.04 RPM
SRP007412_testis	0.11 RPM	35.83 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_940 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_940 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1135

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012225	1 retrocopy	retro_cjac_1234,
Monodelphis domestica	ENSMODG00000019068	3 retrocopies	retro_mdom_1247, retro_mdom_1585, retro_mdom_432,
Otolemur garnettii	ENSOGAG00000029444	1 retrocopy	retro_ogar_1635,
Pan troglodytes	ENSPTRG00000014352	1 retrocopy	retro_ptro_940 ,