RetrogeneDB ID: retro_cpor_819

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_296:103682..104569(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMU1
• Ensembl ID: ENSCPOG00000006212
• Aliases: None
• Description: None

Sequence

>retro_cpor_819
ATGTCGATGGAAATCAATTCCTCAGACGTGATCCGTCTTATTATGCAGTACCTGAAGGAGAACGGTTTACATCAGACTCT
GGCTACATTACAGGAGGAAACCACTGTGTATCTGAATAAAGTGAGCAGTATTGAGAGTTTTGTGGCTGAAATTAATAGTA
GCCACTGGGATACAGTTTTACAGGCTATACAGTCCCTGAGATTGCTGGACAAAACCCTTATTGATCTCTATGAGCAGGTT
GTTTTGCAGTGGATAGAGCTCTGTGAATTGGATGTTGCCAGGTCCATTTTGAGACAAACTGACCCCATGATGATGTTAAA
ACAAGCACTGCCTGAGCAGTATATACATCTGGAGAACCTCCTGGTGAGATCTTATTTTGATCTTGGTGAGGCATACCCAC
AGGGAAGTAGCAAAGAGAAAAAAAGAGCAGTGATTGTGCAGGCCTTAGCTGGGGAAGTCAGTGTAGTGCCTCCATCTCAT
CTCCTGGCACTGCTGTGACAGGCCTTGAAGTGGCGCCATCACCAGGGCTTGCTTCCTTGTGGTGTCACCATTGATTTGTT
TCACAGCAAAGCTGCTGCCCAAGATGTGGAAGAAAAGTTTCCTACACAGCTCAGCGGACATATTAAGTTTGGGCAGAAAT
CGCATGTGGAGTGTGCTCGATTTTCTGCAGATTGTCAGTATCTGGTCACTGGCTCTCTTGATGGATTTTTGAAGTGTGGA
ACTTCACAAATGGAAAACTCAAGAAGGATCTGAAGTACCTGGCCCATGATAATTTCATGATGATGGATGGTACCATTCTC
TGCATGTGATTCAGCAGAATTTCAGAAATATTAGCAACTGGTGCCCAAGATGGAAAAATCAAAATGTGGAAAATTCAGAG
TGGACAG

Alignment

ORF - retro_cpor_819 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.87 %
• Parental protein coverage: 57.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSIEIESSDVIRLIMQYLKENSLHRALATLQEETTVSLNTVDSIESFVADINSGHWDTVLQAIQSLKLPD
          MS.EI.SSDVIRLIMQYLKEN.LH..LATLQEETTV.LN.V.SIESFVA.INS.HWDTVLQAIQSL.L.D
Retrocopy MSMEINSSDVIRLIMQYLKENGLHQTLATLQEETTVYLNKVSSIESFVAEINSSHWDTVLQAIQSLRLLD

Parental  KTLIDLYEQVVLELIELRELGAARSLLRQTDPMIMLKQTQPERYIHLENLLARSYFDPREAYPDGSSKEK
          KTLIDLYEQVVL..IEL.EL..ARS.LRQTDPM.MLKQ..PE.YIHLENLL.RSYFD..EAYP.GSSKEK
Retrocopy KTLIDLYEQVVLQWIELCELDVARSILRQTDPMMMLKQALPEQYIHLENLLVRSYFDLGEAYPQGSSKEK

Parental  RRAAIAQALAGEVSVVPPSRLMALLGQALKWQQHQGLLPPGMTIDLFRGKAAVKDVEEEKFPTQLSRHIK
          .RA.I.QALAGEVSVVPPS.L.ALL.QALKW..HQGLLP.G.TIDLF..KAA..DV.EEKFPTQLS.HIK
Retrocopy KRAVIVQALAGEVSVVPPSHLLALL*QALKWRHHQGLLPCGVTIDLFHSKAAAQDV-EEKFPTQLSGHIK

Parental  FGQKSHVECARFSPDGQYLVTGSVDGFI-EVWNFTTGKIRKDLKYQAQDNFMMMDDAVLCMCFSRDTEML
          FGQKSHVECARFS.D.QYLVTGS.DGF..EVWNFT.GK..KDLKY.A.DNFMMMD...LCM.FSR..E.L
Retrocopy FGQKSHVECARFSADCQYLVTGSLDGFL<EVWNFTNGKLKKDLKYLAHDNFMMMDGTILCM*FSRISEIL

Parental  ATGAQDGKIKVWKIQSGQ
          ATGAQDGKIK.WKIQSGQ
Retrocopy ATGAQDGKIKMWKIQSGQ

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	0.00 RPM	33.53 RPM
SRP017611_kidney	0.00 RPM	66.37 RPM
SRP017611_liver	0.00 RPM	47.01 RPM
SRP040447_lung	0.00 RPM	53.47 RPM
SRP040447_skeletal_muscle	0.00 RPM	35.14 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_819 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_819 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006212	1 retrocopy	retro_cpor_819 ,
Cavia porcellus	ENSCPOG00000010747	2 retrocopies	retro_cpor_1531, retro_cpor_548,
Cavia porcellus	ENSCPOG00000014790	1 retrocopy	retro_cpor_12,
Homo sapiens	ENSG00000122692	1 retrocopy	retro_hsap_457,
Gorilla gorilla	ENSGGOG00000014802	1 retrocopy	retro_ggor_440,
Myotis lucifugus	ENSMLUG00000016097	1 retrocopy	retro_mluc_213,
Monodelphis domestica	ENSMODG00000003439	1 retrocopy	retro_mdom_965,
Ochotona princeps	ENSOPRG00000011389	2 retrocopies	retro_opri_19, retro_opri_741,
Pongo abelii	ENSPPYG00000019140	1 retrocopy	retro_pabe_274,
Pan troglodytes	ENSPTRG00000020853	1 retrocopy	retro_ptro_344,