RetrogeneDB ID: retro_cpor_36

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_2:10075898..10076648(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000003311
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000009085
• Aliases: None
• Description: None

Sequence

>retro_cpor_36
CGAGCAAATGCACCTCACCTAGTTGTACTCCCACTGACCACCCCTTTGGCGGAGACCATCATGAAGGCCCGCTTGAAAGG
AGCGCAGACAGGCCGGAACCTCCTAAAGAAGAAGTCTGACGCCTTAACGCTTCGCTTTCGACAGATCCTGAAGAAGATCA
TTGAGACCAAGATGCTGATGGGCGAGGTGATGAGGGAGGCCGCCTTCTCCCTTGCTGAGGCCAAGTTCACAGGGGACGAC
TTCAGCACCACAGTTATCCAAAATGTAAATAAAGCCCAAGTGAAGATTCGGGCGAAGAAAGATAACGTAGCAGGTGTTAC
TTTGCCGGTCTTCGAACATTACCATGAGGGAACTGACGGTTATGAACTCACTGGTTTAGCCAGAGGTGGGGAACAGCTAG
CTAAACTGAAGAGAAATTATGCCAAAGCTGTGGAGCTGCTGGTGGAGCTGGCTTCGCTGCAGACTTCCTTTGTTACTCTG
GATGAAGCTATTAAGATAACCAACAGGCGTGTAAATGCCATCGAGCATGTTATTATACCTCGGATTGAACGTACCCTTGC
TTACATCATCACAGAGCTGGATGAGAGAGAGCGAGAAGAATTCTATAGGTTAAAGAAAATACAGGAGAAGAAAAAGATTC
TCAAGGAAAAATGCGAGAAGGACTTGGAGCAACGGAGAGCAGCTGGTGAGGTGATGGAGCCTGCAAACCTTCTGGCTGAA
GAGAAGGATGAAGATCTTCTGTTTGAATAG

Alignment

ORF - retro_cpor_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.86 %
• Parental protein coverage: 94.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQTIMKARLKGAQTGRNLLKKKSDALTLRFRQILKKIIETKMLMGEVMREAAFSLAEAKFTAGDFSTTV
          .A.TIMKARLKGAQTGRNLLKKKSDALTLRFRQILKKIIETKMLMGEVMREAAFSLAEAKFT..DFSTTV
Retrocopy LAETIMKARLKGAQTGRNLLKKKSDALTLRFRQILKKIIETKMLMGEVMREAAFSLAEAKFTGDDFSTTV

Parental  IQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDSYELTGLARGGEQLAKLKRNYAKAVELLVELASLQT
          IQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTD.YELTGLARGGEQLAKLKRNYAKAVELLVELASLQT
Retrocopy IQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDGYELTGLARGGEQLAKLKRNYAKAVELLVELASLQT

Parental  SFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELDEREREEFYRLKKIQEKKKILKEKCEKDLEQR
          SFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELDEREREEFYRLKKIQEKKKILKEKCEKDLEQR
Retrocopy SFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELDEREREEFYRLKKIQEKKKILKEKCEKDLEQR

Parental  RAAGEVMEPANLLAEEKDEDLLFE
          RAAGEVMEPANLLAEEKDEDLLFE
Retrocopy RAAGEVMEPANLLAEEKDEDLLFE

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	0.17 RPM	49.52 RPM
SRP017611_kidney	0.42 RPM	34.65 RPM
SRP017611_liver	0.00 RPM	18.24 RPM
SRP040447_lung	0.03 RPM	23.18 RPM
SRP040447_skeletal_muscle	0.07 RPM	18.30 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_36 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_36 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 15 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008240	1 retrocopy	retro_amel_332,
Bos taurus	ENSBTAG00000016309	2 retrocopies	retro_btau_1757, retro_btau_408,
Canis familiaris	ENSCAFG00000016369	2 retrocopies	retro_cfam_1186, retro_cfam_999,
Choloepus hoffmanni	ENSCHOG00000003733	5 retrocopies	retro_chof_1229, retro_chof_2711, retro_chof_54, retro_chof_926, retro_chof_938,
Cavia porcellus	ENSCPOG00000009085	1 retrocopy	retro_cpor_36 ,
Felis catus	ENSFCAG00000011078	1 retrocopy	retro_fcat_632,
Myotis lucifugus	ENSMLUG00000006244	5 retrocopies	retro_mluc_2345, retro_mluc_442, retro_mluc_540, retro_mluc_666, retro_mluc_94,
Macaca mulatta	ENSMMUG00000021418	1 retrocopy	retro_mmul_1159,
Monodelphis domestica	ENSMODG00000009896	5 retrocopies	retro_mdom_1196, retro_mdom_1522, retro_mdom_1730, retro_mdom_390, retro_mdom_594,
Mustela putorius furo	ENSMPUG00000007002	2 retrocopies	retro_mputfur_1381, retro_mputfur_748,
Otolemur garnettii	ENSOGAG00000015052	1 retrocopy	retro_ogar_966,
Sus scrofa	ENSSSCG00000002288	1 retrocopy	retro_sscr_357,
Ictidomys tridecemlineatus	ENSSTOG00000027710	1 retrocopy	retro_itri_383,
Vicugna pacos	ENSVPAG00000005696	1 retrocopy	retro_vpac_232,
Drosophila melanogaster	FBgn0040377	1 retrocopy	retro_dmel_70,