RetrogeneDB ID: retro_cpor_986

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_38:20903187..20904402(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000003565
• Aliases: None
• Description: None

Sequence

>retro_cpor_986
AACAAGGGCTCCACAGCACCCCGAACTTTTTATCTCATTAAAGACATCAAGTTTCTCCTCCATGAACCCATTGTTAACAA
ATTTCAGGAATACAAGGTGTTTGTTCGGAAGCTCCGGAAGGCCTATGGGAAAAGCGAGTGGAACACTTTGGAGCGTCTGA
AGGACAATAAGCCTAACTACAAACTTGACCATATCATCAAGGAGCGGTACCCTACATTCATCGATGCTCTGCGGGATCTG
GATGATGCCCTGTCCATGTGCTTCCTCTTTTCCACCTTCCCACGGACAGGCAAGTGCCACGTGCAGACCATCCACCTGTG
CCACCGGCTTACTGTGGAGTTTCTGCATTACATCATTGCTGCCCATGCCCTGCGAAAGGTCTTCCTGTCCATCAAAGGCA
TTTACTACCAGGCCGAGGTGCTGGGGCAGCCCATTGTGTGGATCACACCCTATGCCTTCTCCCATGATCACCCGACAGAT
GTGGACTACAGGGTCATGGCCACTTTCACTGAGTTCTACAACACCTTACTGGGCTTTGTCAACTTCCGCCTCTACCAGTC
GCTCAACCTCCACTATCCACCAAAGCTCGAGAGTCAGGCCCATACAGAGGTGAAGGCGAGGGAAGATACCTATGCATTGG
ACTCTGAGAGCACCATGGAGAAACTGGTGGCTCTCAGTGCCAGCCTGGCCCGTGTGGTGGTGCCTGCAGCAGAGGAGGAA
ACTGAGGCTGACGAGTTTCCTGCTGATGGCGAAATGGCAGTACAGGAAGAAAATCACAGGAAAGAGCTGTTGGTTCAAGA
AAAACACAAGAAGCTCTTTGAAGGCCTAAAGTTCTTCCTGAACCGTGAGGTGCCCCGAGAGGCCCTGACCTTTATCATCA
GAAGTTTTGGGGGGGACGTGTCCTGGGACAAATCTTTGTGCATTGGGGCCACCTATGATGTCACAGACCCCTGCATTACC
CACCAGATTGTGGATCGGCCTGGACAGCAAACCCCTGTCATCGGCAGGTACTATGTGCAGCCCCAGTGGGTATTTGACTG
TGTCAATGCCCGGCTTCTCCTCCCTGTGGCAGAGTACTTTTCAGGGGTGCAGCTACCCCCGCACCTTTCACCCTTCGTGT
CTGAGAAGGAAGGGGATTATATTCCACCAGAGAAGCTGAAGCTGCTGGTTCTTCAGCGAGGAGAGGATCCAGGAAACTTG
AAAGAGTCAGAAGAT

Alignment

ORF - retro_cpor_986 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.3 %
• Parental protein coverage: 69.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NKGSTAPRTFYLIKDIKFLLHEPIVNKFREYKVFVRKLRKAYGKSEWNTVERLKDNKPNYKLDHIIKERY
          NKGSTAPRTFYLIKDIKFLLHEPIVNKF.EYKVFVRKLRKAYGKSEWNT.ERLKDNKPNYKLDHIIKERY
Retrocopy NKGSTAPRTFYLIKDIKFLLHEPIVNKFQEYKVFVRKLRKAYGKSEWNTLERLKDNKPNYKLDHIIKERY

Parental  PTFIDALRDLDDALSMCFLFSTFPRTGKCHVQTIHLCRRLTVEFLHYIIAARALRKVFLSIKGIYYQAEV
          PTFIDALRDLDDALSMCFLFSTFPRTGKCHVQTIHLC.RLTVEFLHYIIAA.ALRKVFLSIKGIYYQAEV
Retrocopy PTFIDALRDLDDALSMCFLFSTFPRTGKCHVQTIHLCHRLTVEFLHYIIAAHALRKVFLSIKGIYYQAEV

Parental  LGQPIVWITPYAFSHDHPTDVDYRVMATFTEFYTTLLGFVNFRLYQSLNLHYPPKLESQAQTEVKAKEDT
          LGQPIVWITPYAFSHDHPTDVDYRVMATFTEFY.TLLGFVNFRLYQSLNLHYPPKLESQA.TEVKA.EDT
Retrocopy LGQPIVWITPYAFSHDHPTDVDYRVMATFTEFYNTLLGFVNFRLYQSLNLHYPPKLESQAHTEVKAREDT

Parental  YALDSESAMEKLAALSASLARVVVPAAEEEAEADEFPADGEMAVQEENRRKELLAQEKHKKLFEGLKFFL
          YALDSES.MEKL.ALSASLARVVVPAAEEE.EADEFPADGEMAVQEEN.RKELL.QEKHKKLFEGLKFFL
Retrocopy YALDSESTMEKLVALSASLARVVVPAAEEETEADEFPADGEMAVQEENHRKELLVQEKHKKLFEGLKFFL

Parental  NREVPREALTFIIRSFGGDVSWDKSLCIGATYDVTDPCITHQIVDRPGQQTPVIGRYYVQPQWVFDCVNA
          NREVPREALTFIIRSFGGDVSWDKSLCIGATYDVTDPCITHQIVDRPGQQTPVIGRYYVQPQWVFDCVNA
Retrocopy NREVPREALTFIIRSFGGDVSWDKSLCIGATYDVTDPCITHQIVDRPGQQTPVIGRYYVQPQWVFDCVNA

Parental  RLLLPVAEYFPGVQLPPHLSPFVSEKEGDYIPPEKLKLLALQRGEDPGNLKESEE
          RLLLPVAEYF.GVQLPPHLSPFVSEKEGDYIPPEKLKLL.LQRGEDPGNLKESE.
Retrocopy RLLLPVAEYFSGVQLPPHLSPFVSEKEGDYIPPEKLKLLVLQRGEDPGNLKESED

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	34.22 RPM
SRP017611_kidney	0.00 RPM	46.80 RPM
SRP017611_liver	0.00 RPM	30.95 RPM
SRP040447_lung	0.08 RPM	56.85 RPM
SRP040447_skeletal_muscle	0.03 RPM	25.95 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_986 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_986 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010617	1 retrocopy	retro_cjac_3182,
Cavia porcellus	ENSCPOG00000003565	1 retrocopy	retro_cpor_986 ,
Homo sapiens	ENSG00000100029	1 retrocopy	retro_hsap_4133,
Mus musculus	ENSMUSG00000020430	2 retrocopies	retro_mmus_1393, retro_mmus_3225,
Otolemur garnettii	ENSOGAG00000005804	1 retrocopy	retro_ogar_1719,
Pongo abelii	ENSPPYG00000011716	1 retrocopy	retro_pabe_3471,
Pan troglodytes	ENSPTRG00000014251	2 retrocopies	retro_ptro_2018, retro_ptro_2809,
Rattus norvegicus	ENSRNOG00000004515	2 retrocopies	retro_rnor_2953, retro_rnor_824,
Tupaia belangeri	ENSTBEG00000009825	1 retrocopy	retro_tbel_1000,