RetrogeneDB ID: retro_cpor_410

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_146:2036569..2037822(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3L
• Ensembl ID: ENSCPOG00000005885
• Aliases: None
• Description: None

Sequence

>retro_cpor_410
TACCCAGGCGACTATGATATGCACACAGGAGATCCAAAGCAGGACCTTGCTTATGAACACCAGTATGAACAACAGACCTA
TCAGGTGATCCCTGAAGTGATCAAAAACTTCATCCAGTATTTCCACAAAACTGTCTCAGATTTGATTGACCAGAAGGTAT
ACGAGCTTCAGGCCAGTCGCGTCTCTAGTGATGTCATTGACCAGAAGGTGTATGAGATCCAGGACATCTATGAGAACAGC
TGGACCAAGCTGACTGAAAGATTCTTTAAGAATACTCCTTGGCCTGAGGCTGAAGCCATTGCTCCATAGGTTGGCAACGA
TGCTGTCTTCCTGATTTTGTACAAAGAATTATATTACAGACACATATATGCCAAAGTCAGTGGGGGACCCTCCTTAGAGC
AGAGGTTTGAGTCGTATTACAACTGCTGCAACCTCTTCAACTACATCCTCAATGCAGATGGGCCCGCCCCCCTTGAACTG
CCAAACCAGTGGCTCTGGGATATCATCAATGAATTCATCTACCAGTTCCAGTCATTTAGTCAGTACCGTTGTAAGACCGC
CAAGAAGTCAGAGGAGGAGATTGACTTCCTGCGATCCAACCCCAAAATCTGGAATGTCCACAGTGTCCTCAACGTCCTTC
ACTCCCTGGTGGACAAATCCAACATCAACCGGCAGCTGGAGGTGTACACGAGTGGAGGTGACCCAAGAGCATGGCCAGAG
AGTATGGACATCACTCCCTCTACAAGATGCTAGGCTACTTCAGCCTGGTGGGGCTGCTGCGCCTGCACTCGCTGCTGGGG
GATTAGTACCAGGCCATCAAGGTGCTGGAGAACATTGAGCTGAACAAGAAAAGCATGTACTCCCGTGTGCCTGAGTGCCA
GGTCACCACCTACTACTATGTGGGGTTTGCGTATTTGATGATGCGGCGCTACCAGGATGCCATCCGGGTCTTTGCCAACA
TCCTCCTCTACATCCAGAGGACCAAGAGCATGTTCCAGAGGACCACGTACAAGTATGAGATGATCAACAAGCAGAACGAG
CAGATGCACGCGCTGCTGGCCATCGCCCTCACCATGTACCCCATGTGGATCGAGGAGAGCATCCACCTGCAGCTGCGGGA
GAAATACGGGGACAAAATGCTGCGCATGCAGGAGGGCGACCCGCAGGTCTACGAGGAGCTCTTCAGCTACTCCTGCCCCA
AGTTCCTGTCGCCCGTGGTGCCCAACTACGACAACGTGCACCCTAGCTACCAC

Alignment

ORF - retro_cpor_410 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.66 %
• Parental protein coverage: 69.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YPGDYDMHTGDPKQDLAYERQYEQQTYQVIPEVIKNFIQYFHKTVSDLIDQKVYELQASRVSSDVIDQKV
          YPGDYDMHTGDPKQDLAYE.QYEQQTYQVIPEVIKNFIQYFHKTVSDLIDQKVYELQASRVSSDVIDQKV
Retrocopy YPGDYDMHTGDPKQDLAYEHQYEQQTYQVIPEVIKNFIQYFHKTVSDLIDQKVYELQASRVSSDVIDQKV

Parental  YEIQDIYENSWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLILYKELYYRHIYAKVSGGPSLEQRFESYY
          YEIQDIYENSWTKLTERFFKNTPWPEAEAIAP.VGNDAVFLILYKELYYRHIYAKVSGGPSLEQRFESYY
Retrocopy YEIQDIYENSWTKLTERFFKNTPWPEAEAIAP*VGNDAVFLILYKELYYRHIYAKVSGGPSLEQRFESYY

Parental  NYCNLFNYILNADGPAPLELPNQWLWDIIDEFIYQFQSFSQYRCKTAKKSEEEIDFLRSNPKIWNVHSVL
          N.CNLFNYILNADGPAPLELPNQWLWDII.EFIYQFQSFSQYRCKTAKKSEEEIDFLRSNPKIWNVHSVL
Retrocopy NCCNLFNYILNADGPAPLELPNQWLWDIINEFIYQFQSFSQYRCKTAKKSEEEIDFLRSNPKIWNVHSVL

Parental  NVLHSLVDKSNINRQLEVYTSGGD-PESVAGEYGRHSLYKMLGYFSLVGLLRLHSLLGDYYQAIKVLENI
          NVLHSLVDKSNINRQLEVYTSGGD.P.S.A.EYG.HSLYKMLGYFSLVGLLRLHSLLGD.YQAIKVLENI
Retrocopy NVLHSLVDKSNINRQLEVYTSGGD<PKSMAREYGHHSLYKMLGYFSLVGLLRLHSLLGD*YQAIKVLENI

Parental  ELNKKSMYSRVPECQVTTYYYVGFAYLMMRRYQDAIRVFANILLYIQRTKSMFQRTTYKYEMINKQNEQM
          ELNKKSMYSRVPECQVTTYYYVGFAYLMMRRYQDAIRVFANILLYIQRTKSMFQRTTYKYEMINKQNEQM
Retrocopy ELNKKSMYSRVPECQVTTYYYVGFAYLMMRRYQDAIRVFANILLYIQRTKSMFQRTTYKYEMINKQNEQM

Parental  HALLAIALTMYPMRIDESIHLQLREKYGDKMLRMQKGDPQVYEELFSYSCPKFLSPVVPNYDNVHPNYH
          HALLAIALTMYPM.I.ESIHLQLREKYGDKMLRMQ.GDPQVYEELFSYSCPKFLSPVVPNYDNVHP.YH
Retrocopy HALLAIALTMYPMWIEESIHLQLREKYGDKMLRMQEGDPQVYEELFSYSCPKFLSPVVPNYDNVHPSYH

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	0.06 RPM	45.50 RPM
SRP017611_kidney	0.21 RPM	92.33 RPM
SRP017611_liver	0.09 RPM	48.49 RPM
SRP040447_lung	0.03 RPM	90.14 RPM
SRP040447_skeletal_muscle	0.10 RPM	83.63 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_410 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_410 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005885	2 retrocopies	retro_cpor_1288, retro_cpor_410 ,
Homo sapiens	ENSG00000100129	1 retrocopy	retro_hsap_1369,
Monodelphis domestica	ENSMODG00000019068	3 retrocopies	retro_mdom_1247, retro_mdom_1585, retro_mdom_432,
Otolemur garnettii	ENSOGAG00000029444	1 retrocopy	retro_ogar_1635,