RetrogeneDB ID: retro_cpor_898

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_32:1174459..1175143(-)
• Located in intron of: ENSCPOG00000015691

Retrocopy information

• Ensembl ID: ENSCPOG00000022472
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EAPP
• Ensembl ID: ENSCPOG00000003005
• Aliases: None
• Description: None

Sequence

>retro_cpor_898
TCAGAGAGTGTCTTAACTGGGGAAAGTGAGTCCTCTAGTGAAGATGAGTTAAATTCCACCATAAAAACAATGGAGGACAA
ACTCTCTTCCCTTGGAACAGGATCTTCCTCAGGAAATGGAAATGTGGGAATAGCTCCAGCAAAGTACTATGATGATATAT
ATTTTGATTCTGATTCTGAGAATGAAGACAAAGCACAGGTAAAAAAGAAGAAAATGAAGAGACGACACAGAATTCTAACA
AATGATGAATTGCTATATGAACCTGATAAAGATAACAGAGACCAGGCATGGGTTAATGCACAGAGAAGAGGCTTTCATGG
TTTTGGACTACAGAGACAGCAACTGGCAGTTCCTAACAGTGATGCTGTCTTAAATTGCCCTGCTTGTATGACTACATTGT
GCCTCGATTGCCAAAGGCATGAATCTTACAAAACTCAGTACAAAGCAATGTTTGTGATGAACTGTTCCATCAACAGAGAG
GAGATACTAAGATACAAAAACCCAGACAACAGAAAGAAGAGATGGGGCTACAAGAAGCTGCGATCTAACCAGGAAGATCC
CATGAAGCAGACCGAAGCTGAAGAACTCTACCGCCCTGTGATGTGCGCAGAGTGTTCCCCTGAAGTGGCTGTCTATGACA
AGGACGAAGTCTTTCACTTTTTCAATGTTTTAGCAAGCCATTCT

Alignment

ORF - retro_cpor_898 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 81.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SESSSEDEFEKEMEAELNSTIKTMEDKLSSLGTGSSSGNGNVGIAPAKYYDDVYFDSDSEDEDKAAQVTK
          SES....E.E...E.ELNSTIKTMEDKLSSLGTGSSSGNGNVGIAPAKYYDD.YFDSDSE.EDKA.QV.K
Retrocopy SESVLTGESESSSEDELNSTIKTMEDKLSSLGTGSSSGNGNVGIAPAKYYDDIYFDSDSENEDKA-QVKK

Parental  KKKKRRHRILTNDELLYDPDKDNRDQAWVDAQRRGYHGFGLQRPRQQQQPVPNSDAVLNCPACMTTLCLD
          KK.KRRHRILTNDELLY.PDKDNRDQAWV.AQRRG.HGFGLQR...QQ..VPNSDAVLNCPACMTTLCLD
Retrocopy KKMKRRHRILTNDELLYEPDKDNRDQAWVNAQRRGFHGFGLQR---QQLAVPNSDAVLNCPACMTTLCLD

Parental  CQRHESYKTQYRAMFVMNCSINREEVLRYKNPDNRKKRRGYKKLRSNQEDPKKQTEAEEIYHPVMCAECS
          CQRHESYKTQY.AMFVMNCSINREE.LRYKNPDNRKKR.GYKKLRSNQEDP.KQTEAEE.Y.PVMCAECS
Retrocopy CQRHESYKTQYKAMFVMNCSINREEILRYKNPDNRKKRWGYKKLRSNQEDPMKQTEAEELYRPVMCAECS

Parental  TEVAVYDKDEVFHFFNVLASHS
          .EVAVYDKDEVFHFFNVLASHS
Retrocopy PEVAVYDKDEVFHFFNVLASHS

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	16.39 RPM
SRP017611_kidney	0.00 RPM	22.40 RPM
SRP017611_liver	0.00 RPM	16.45 RPM
SRP040447_lung	0.05 RPM	23.71 RPM
SRP040447_skeletal_muscle	0.00 RPM	9.74 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_898 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_898 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005391	1 retrocopy	retro_cjac_3231,
Cavia porcellus	ENSCPOG00000003005	1 retrocopy	retro_cpor_898 ,
Myotis lucifugus	ENSMLUG00000013814	1 retrocopy	retro_mluc_596,
Monodelphis domestica	ENSMODG00000014525	1 retrocopy	retro_mdom_1226,
Mustela putorius furo	ENSMPUG00000001029	1 retrocopy	retro_mputfur_19,
Oryctolagus cuniculus	ENSOCUG00000003226	1 retrocopy	retro_ocun_1701,
Ictidomys tridecemlineatus	ENSSTOG00000005273	2 retrocopies	retro_itri_1598, retro_itri_237,
Tupaia belangeri	ENSTBEG00000001306	1 retrocopy	retro_tbel_4258,