RetrogeneDB ID: retro_cpor_1288

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_65:9137048..9138502(+)
• 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_1288
AAACTCTTCACCCACTATTTCCACAAAACTGTCTCAGATTTGATTGACCAGAAGGTATACGAGCTTCAGGCCAGTCGCAT
CTCTAGTGATGTCATTGACCAGAAGGTGTATGAGATCCAGGACATCTATGAGAACAGCTGGACCAAGCTGACTAAAAGAT
TCTTTAACAATACTACTTGGCCTGAGGCCGAAGCCATAGCTCCACAGGTTGGCAACGATGCTGTCTTCCTGATTTTGTAC
AAAGAATTATATTACAGACACATATATGCCAAAGTCAGAGGGGGACCCTCCTTACAGCAGAGGTTTGAGTCCTCTTACAA
CTACTGCAACCTCTTCAACTACATCCTCAGTGCAGATGGGCCTGCCCCCCTTAAACTGCCCAACCAGTGGCTCTGGGATA
TCATCGATGAATTTATGTACCAGTTCCAGTCATTTAGTCAGTACCACTGTAAGACGGCCAAGAAGTCAGAGGAGGAGATT
GATTTCCTGTGATCCAACCCCAAAATCTGGAATGTCCACAGTGTCCTCAACATCCTTCACTCCCTGGTGGACAAATCCAA
CATCAACCGGCAGCTGGAGGTGTACACGAGCGGAGGTGACCCCGAGAGTGTGGCAGGGGAGTATGGATGTCACTCCCTCT
ACAAGATGCTGGGCTACTTCAGCCTAGTGGGACTGCTGCACCTGCACTCGCTGCTGGGGGATTACTACCAGGCCATCAAG
GTGCTGGAGAACATTGAGCTGAACAAAAAGAGTATGTACTCCCGTGTGCCCGAGTGCCAGGTCACCACCTACTACTATGT
GGGGTTTGCATATTTGATGATGCGACGCTACCAGGATGCCATCTGGGTCTTTGCCAACATCCTCCTTTACATCCAGAGGA
CCAAGAGCATGTTCCAGAGGACCACGTACAAGTATGAGATGATCAACAAGCAGAACGAGCAGATGCACGCGCTGCTGGCC
ATCGCCCTCACCAGGTACCCCATGCGGATGGACGAGAGCATCCACCTGCAGCTGCGGGAGAAGTATGGGGACAAAATGCT
GCGCATGCAGAAGGGCGACCCGCAGGTCTACGAGGAGCTCTTCAGCTACTCCTGCCCCAAGTTCCTGTCACCCATGGACA
ACGTGCACCCTAACTACCACAAGGAGCCCTTCCTGCAGCAGCTCAAGGTGTTCTCCAACGAGGTGCAGCAGCAGGCCCAG
CTCTCACCATCCGCAGCTTCCTCAAGCTCTACACCACCATGCCTGTGGCCAAGCTGGCTGGCTTCCTGGACCTCACTGAG
CAGGAGTTCCGCATTCAGCTGCTTGTCTTCAAGCACAAGATGAAGAACCTAGTGTGGACCAGTGGCATCTCCACCCTGGA
CGGCGAGTTCCAGTCTGCTTCTGAGGTGGACTTCTACATCAATAAGGACATGATCCACACCTCAGACACCAAGGTTGCCA
GAAGAAGATGGGAC

Alignment

ORF - retro_cpor_1288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.86 %
• Parental protein coverage: 81.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KNFIQYFHKTVSDLIDQKVYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPEAEAIAPQV
          K.F..YFHKTVSDLIDQKVYELQASR.SSDVIDQKVYEIQDIYENSWTKLT.RFF.NT.WPEAEAIAPQV
Retrocopy KLFTHYFHKTVSDLIDQKVYELQASRISSDVIDQKVYEIQDIYENSWTKLTKRFFNNTTWPEAEAIAPQV

Parental  GNDAVFLILYKELYYRHIYAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPNQWLWDIIDEFIY
          GNDAVFLILYKELYYRHIYAKV.GGPSL.QRFES.YNYCNLFNYIL.ADGPAPL.LPNQWLWDIIDEF.Y
Retrocopy GNDAVFLILYKELYYRHIYAKVRGGPSLQQRFESSYNYCNLFNYILSADGPAPLKLPNQWLWDIIDEFMY

Parental  QFQSFSQYRCKTAKKSEEEIDFLRSNPKIWNVHSVLNVLHSLVDKSNINRQLEVYTSGGDPESVAGEYGR
          QFQSFSQY.CKTAKKSEEEIDFL.SNPKIWNVHSVLN.LHSLVDKSNINRQLEVYTSGGDPESVAGEYG.
Retrocopy QFQSFSQYHCKTAKKSEEEIDFL*SNPKIWNVHSVLNILHSLVDKSNINRQLEVYTSGGDPESVAGEYGC

Parental  HSLYKMLGYFSLVGLLRLHSLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAYLMMRRYQDA
          HSLYKMLGYFSLVGLL.LHSLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAYLMMRRYQDA
Retrocopy HSLYKMLGYFSLVGLLHLHSLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAYLMMRRYQDA

Parental  IRVFANILLYIQRTKSMFQRTTYKYEMINKQNEQMHALLAIALTMYPMRIDESIHLQLREKYGDKMLRMQ
          I.VFANILLYIQRTKSMFQRTTYKYEMINKQNEQMHALLAIALT.YPMR.DESIHLQLREKYGDKMLRMQ
Retrocopy IWVFANILLYIQRTKSMFQRTTYKYEMINKQNEQMHALLAIALTRYPMRMDESIHLQLREKYGDKMLRMQ

Parental  KGDPQVYEELFSYSCPKFLSPVVPNYDNVHPNYHKEPFLQQLKVFSDEVQQQAQLS-TIRSFLKLYTTMP
          KGDPQVYEELFSYSCPKFLSP.....DNVHPNYHKEPFLQQLKVFS.EVQQQAQLS.TIRSFLKLYTTMP
Retrocopy KGDPQVYEELFSYSCPKFLSPM----DNVHPNYHKEPFLQQLKVFSNEVQQQAQLS<TIRSFLKLYTTMP

Parental  VAKLAGFLDLTEQEFCIQLLVFKHKMKNLVWTSGISALDGEFQSASEVDFYIDKDMIHIADTKVARRYGD
          VAKLAGFLDLTEQEF.IQLLVFKHKMKNLVWTSGIS.LDGEFQSASEVDFYI.KDMIH..DTKVARR..D
Retrocopy VAKLAGFLDLTEQEFRIQLLVFKHKMKNLVWTSGISTLDGEFQSASEVDFYINKDMIHTSDTKVARRRWD

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	1.15 RPM	45.50 RPM
SRP017611_kidney	0.00 RPM	92.33 RPM
SRP017611_liver	0.04 RPM	48.49 RPM
SRP040447_lung	0.35 RPM	90.14 RPM
SRP040447_skeletal_muscle	0.28 RPM	83.63 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1288 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1288 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,