RetrogeneDB ID: retro_cpor_408

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_145:2143896..2144360(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMNDC1
• Ensembl ID: ENSCPOG00000006335
• Aliases: None
• Description: None

Sequence

>retro_cpor_408
ATGTCAGAGGATGTAGTAAAGCAGCCAGCAAGTTACAAAGCTCAGCTCCATCAAGTAGAAGCTTCATTATCTGGAAATGA
AGAAAATGAAGATTTGCTAAAATTGAAGAAAGATTTACTAAAAGTTATAGAATTAACCAAAGTACTGTCGATTCCAACTT
AAGAAACTCTTACAAGTTCAGATAGTTTTGCTTATACTTAGCCCACTCATTCATGAAAGACAGGAGACAAGTGTACGGCA
ATTGGAGTGAAGATGGACAGTGTTATGAAGCAGAGATTGAGAAGAGAGATGAAGAAAATGGCACCATTGCAATCATCTTT
GCTGGTTATGGCAATGCTGAAGTTATTCTTCTGTTGAACCTCAAGTCTGTAGAAGAAGGAAAAAAGGCAGTGGAGGATAG
TGGTACCAAACCCAGGTGTAAAAAAGAAATGATTTCCCAACAGCATGAATATGAAAAGAATAAA

Alignment

ORF - retro_cpor_408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.8 %
• Parental protein coverage: 69.96 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSEDLAKQLASYKAQLQQVEAALSGNGENEDLLKLKKDLQEVIELTKDLLSTQPSETLTSSDSFASTQPT
          MSED..KQ.ASYKAQL.QVEA.LSGN.ENEDLLKLKKDL..VIELTK..LS....ETLTSSDSFA.T.PT
Retrocopy MSEDVVKQPASYKAQLHQVEASLSGNEENEDLLKLKKDLLKVIELTK-VLSIPT*ETLTSSDSFAYT*PT

Parental  HSWKVGDKCMAI-WSEDGQCYEAEIEEIDEENGTAAITFAGYGNAEVTPLLNLKPVEEGRKAKEDSGSKP
          HS.K.GDKC.AI.WSEDGQCYEAEIE..DEENGT.AI.FAGYGNAEV..LLNLK.VEEG.KA.EDSG.KP
Retrocopy HS*KTGDKCTAI<WSEDGQCYEAEIEKRDEENGTIAIIFAGYGNAEVILLLNLKSVEEGKKAVEDSGTKP

Parental  MSKKEMIAQQRELEQER
          ..KKEMI.QQ.E.E...
Retrocopy RCKKEMISQQHEYEKNK

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	8.80 RPM
SRP017611_kidney	0.00 RPM	9.32 RPM
SRP017611_liver	0.00 RPM	8.71 RPM
SRP040447_lung	0.00 RPM	12.18 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.78 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_408 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_408 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006335	1 retrocopy	retro_cpor_408 ,
Macaca mulatta	ENSMMUG00000007775	2 retrocopies	retro_mmul_1972, retro_mmul_2419,
Tarsius syrichta	ENSTSYG00000006636	1 retrocopy	retro_tsyr_965,