RetrogeneDB ID: retro_cpor_716

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_25:5342676..5343077(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN7
• Ensembl ID: ENSCPOG00000000183
• Aliases: None
• Description: None

Sequence

>retro_cpor_716
GTGGCTTCGAGGAGAATGGAGACCCAGCCTGTGATGCCCTGTCTCGAAACCCTCCTCCTCACTCGCTCCTCTGGCTTCTG
AATCATGGGGCTGATGCGGTTGGCTATTGGAGTCTGGGACATCTTCCTCTGGGCACCTACGTCTCCCTTACTGCTGAAAA
CTCCACGAATGCTCCCTCCGTGCTCCTGAGAACTGGCACCATTGTTGCTTTTGGCTTGCTTGGGTGCTTGGCAGTGTGCC
GTGGTAACCCGTGGGTGCTGAAAGTGTATGCAGCGTTTCTGTCCCTGAGGCTCCTGTTTGAGCTCAAAGCTGGCATTTCA
GGGTTTGTGCTCCATTGCGAGATCAAGGACACCTTGCCGAGGACTCACACAAATGCCATGCAGAACAACAAGGGCAAGGA
G

Alignment

ORF - retro_cpor_716 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.71 %
• Parental protein coverage: 54.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASRRMETKPVITCLKTLLIIYSFVFWITGVILLAVGVW-GKLTLGTYISLIAENSTNAPYVLIGTGTTI
          .ASRRMET.PV..CL.TLL...S..F.I.G...LA.GVW.G.L.LGTY.SL.AENSTNAP.VL..TGT.I
Retrocopy VASRRMETQPVMPCLETLLLTRSSGF*IMGLMRLAIGVW<GHLPLGTYVSLTAENSTNAPSVLLRTGT-I

Parental  VVFGLFGCFATCRGSPWMLKLYAMFLSLVFLAELVAGISGFVFRHEIKDTFLRTYTDAMQNYNGND
          V.FGL.GC.A.CRG.PW.LK.YA.FLSL..L.EL.AGISGFV...EIKDT..RT.T.AMQN..G..
Retrocopy VAFGLLGCLAVCRGNPWVLKVYAAFLSLRLLFELKAGISGFVLHCEIKDTLPRTHTNAMQNNKGKE

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	0.12 RPM	304.72 RPM
SRP017611_kidney	0.00 RPM	73.39 RPM
SRP017611_liver	0.00 RPM	61.90 RPM
SRP040447_lung	0.00 RPM	90.39 RPM
SRP040447_skeletal_muscle	0.00 RPM	72.83 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_716 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_716 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000183	1 retrocopy	retro_cpor_716 ,
Cavia porcellus	ENSCPOG00000009142	1 retrocopy	retro_cpor_676,
Dipodomys ordii	ENSDORG00000012580	1 retrocopy	retro_dord_708,
Macropus eugenii	ENSMEUG00000002809	1 retrocopy	retro_meug_1563,
Otolemur garnettii	ENSOGAG00000008547	2 retrocopies	retro_ogar_1615, retro_ogar_3124,