RetrogeneDB ID: retro_cpor_339

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_13:21913625..21914372(+)
• 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_339
GGTCATGGGTGAGTCAGCACCAGGCTCCTGTTCAACTCACTGGTATCCATCTGCATTGTGTTCCTCAGCAAATGGATCTG
TGTGCACCACAGCATGAGCTTGACCCTGGTACAACTCATAGTCACCTGGTTGGGCTTGTACGTCTACCAGAAGCTGTACA
ACTTTGACCACCAAATTATACCCTCTCCAAGCTCCTCCTCCTGGCTCTGAGCGTGTGTGGCTTCATCATCTTCCTCAGCT
CTCTCAGCAGAGCAGCACCAAGGACACCTAGCAGCTGGCCAAGGCCATGGCCGAGTGGTGATTACAGCCATCCAGACCGT
GTGCTACCAGGACAGCTTTGCCACAGGACTGAGGCTCACAATGATTCCTAGAATACTTTAGTGTAATCTAAATTCTTAGT
AAGATGTGAAGGTTAATTCCTTGGAAAGATGTTTGCTGCTCGTGGTGTTTTAGTTACAACTCTTTGTTAAGTGTGTGTCA
GGGCCAAACAGCAAGGGCTGGGAGTGTACTCAGGGCTGTTGTTCTTCTTCTAGGCTTCAGTGTCATCTCCTGTGTTGCTG
GTCACTGTGCCTTCCTTTGAGCCAGTGTTTGGAGAGGGAGGAGCCCTTGGTCCCTGGTCTGTTTCTGCTGTGCTTCTGGT
GCTGCTGTGTGGAGTAAATGCTTCAAGATGAACTCAGATACTTACTGGTCACTGGGAACATTTTGCTCGTCACCTGTCAC
ATATTTGTACACTTCTAGTTTATATTA

Alignment

ORF - retro_cpor_339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.85 %
• Parental protein coverage: 81.15 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GHGRIVAGLLFNLLVSICIVFLNKWIYVHHGFPNMSLTLVHFVVTWLGLYICQKLDIFAPKSLPP-SKLL
          GHG.....LLFN.LVSICIVFL.KWI.VHH....MSLTLV...VTWLGLY..QKL..F.....P..SKLL
Retrocopy GHG*VSTRLLFNSLVSICIVFLSKWICVHH---SMSLTLVQLIVTWLGLYVYQKLYNFDHQIIPS<SKLL

Parental  LLALSFCGFVVFTN-LSLQNNTIGTYQLAKAMTT-PVIIAIQTLCYQKSFSTRIQLTLIPITLGVILNSY
          LLALS.CGF..F...LS.Q..T..T.QLAKAM....VI.AIQT.CYQ.SF.T...LT.IP..L...LNS.
Retrocopy LLALSVCGFIIFLS<LSQQSSTKDT*QLAKAMAE<VVITAIQTVCYQDSFATGLRLTMIPRIL*CNLNS*

Parental  YDVKFN-FLGMVFAALGVLVTSLYQVWVGAKQHELQVNSMQLLYYQAPMSSAMLLVAVPFFEPVFGEGGI
          .DVK.N.FLG..FAA.GVLVT.L..V.V.AKQ..L.V.S..L....A..SS..LLV.VP.FEPVFGEGG.
Retrocopy *DVKVN<FLGKMFAARGVLVTTLC*VCVRAKQQGLGVYSGLLFFF*ASVSSPVLLVTVPSFEPVFGEGGA

Parental  FGPWSVSAVLMVLLSGVIA-FMVNLSIYW-IIGNTSPVTYNMFGHFKFCI
          .GPWSVSAVL.VLL.GV.A.F..N...YW...GN...VT...F.HF.F..
Retrocopy LGPWSVSAVLLVLLCGVNA<FKMNSDTYW<VTGNILLVTCHIFVHF*FIL

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	0.52 RPM	5.18 RPM
SRP017611_kidney	3.25 RPM	4.19 RPM
SRP017611_liver	0.04 RPM	13.54 RPM
SRP040447_lung	0.00 RPM	3.86 RPM
SRP040447_skeletal_muscle	0.13 RPM	1.52 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_339 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_339 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,