RetrogeneDB ID: retro_cpor_1404

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_8:42776064..42776708(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35E3
• Ensembl ID: ENSCPOG00000004322
• Aliases: None
• Description: None

Sequence

>retro_cpor_1404
GCACAGCTGGCTGAGCAACTCCGGAGCCTCTGGCAAAGAGTTGCAGGACTCCTGTTCAATCTTCTGGTGTCCATCTGCAC
CATGTTCCTCAATAAGTGGATCTATGTCCTCCATGGCTTCCAGAGCATGAGCCCAACCTTGGTACAGCTCATGGTCAGCT
GGCTAGACTTGTCCATCTTCCAGAAGCTGGACATTTTTGTCTCCCGAAAAGTCTGCATGCTTTCCAACCTCTTCCTCCTA
GCTATGAGCTCGTGTGACTTAGTGGTCTCTTCAGCCTGTTTCAACAGAATAACATCATCAGCACCTATCAGCTGACTAAA
GCCATGACTGCAGCTGTGACTGTAGCCATCAGGCCTTATGATTCCAAAAGAGCTTCTCCAGGAGAATTCAGCTCATGCGG
ACTCCTATAACTTTAGGTATAATTTTAAATTCTTATTACAATGTGAATTTTTAATTTACTTGAAATAGTGTGGGCAGCTC
TTGTTGTTTTAGTTATGTATCTTTTTCAAGTGTGTGTAGGGACCAAACAATATGAGTTACGAGTAAACATAACACAGTTA
CTGTGTTATCAGGCTCCAATGTTGTCTGCTACAATGCTGGTTGCTGTGACCTCTGAGCCAGCATTTGGAGAGGGAGGAAT
ATTT

Alignment

ORF - retro_cpor_1404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.56 %
• Parental protein coverage: 68.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASLAERVRGHGRIVAGLLFNLLVSICIVFLNKWIYVHHGFPNMSLTLVHFVVTWLGLYICQKLDIFAPKS
          A.LAE..R.....VAGLLFNLLVSIC..FLNKWIYV.HGF..MS.TLV...V.WL.L.I.QKLDIF....
Retrocopy AQLAEQLRSLWQRVAGLLFNLLVSICTMFLNKWIYVLHGFQSMSPTLVQLMVSWLDLSIFQKLDIFVSRK

Parental  L-PPSKLLLLALSFCGFVVFT-NLSLQNNTIGTYQLAKAMTTPVIIAI-QTLCYQKSFSTRIQLTLIPIT
          ....S.L.LLA.S.C..VV....L..QNN.I.TYQL.KAMT..V..AI.Q.L..QKSFS.RIQL...PIT
Retrocopy VCMLSNLFLLAMSSCDLVVSS<SLFQQNNIISTYQLTKAMTAAVTVAI<QAL*FQKSFSRRIQLMRTPIT

Parental  LGVILNSYYDVK-FNFLGMVFAALGVLVTSLYQVWVGAKQHELQVNSMQLLYYQAPMSSAMLLVAVPFFE
          LG.ILNSYY.V..FN.L..V.AAL.VLV..L.QV.VG.KQ.EL.VN..QLL.YQAPM.SA..LVAV...E
Retrocopy LGIILNSYYNVN>FNLLEIVWAALVVLVMYLFQVCVGTKQYELRVNITQLLCYQAPMLSATMLVAVT-SE

Parental  PVFGEGGIF
          P.FGEGGIF
Retrocopy PAFGEGGIF

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	5.18 RPM
SRP017611_kidney	0.00 RPM	4.19 RPM
SRP017611_liver	0.00 RPM	13.54 RPM
SRP040447_lung	0.00 RPM	3.86 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.52 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1404 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1404 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031919	1 retrocopy	retro_btau_642,
Choloepus hoffmanni	ENSCHOG00000013347	1 retrocopy	retro_chof_2348,
Cavia porcellus	ENSCPOG00000004322	3 retrocopies	retro_cpor_1404 , retro_cpor_1487, retro_cpor_339,
Homo sapiens	ENSG00000175782	1 retrocopy	retro_hsap_513,
Gorilla gorilla	ENSGGOG00000012605	1 retrocopy	retro_ggor_473,
Mus musculus	ENSMUSG00000060181	1 retrocopy	retro_mmus_287,
Pan troglodytes	ENSPTRG00000005201	1 retrocopy	retro_ptro_383,
Pteropus vampyrus	ENSPVAG00000002545	1 retrocopy	retro_pvam_710,