RetrogeneDB ID: retro_cpor_510

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_176:46760..48199(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDAD1
• Ensembl ID: ENSCPOG00000008524
• Aliases: None
• Description: None

Sequence

>retro_cpor_510
AATGATGCCAAAATGGTCAATGTTACCATGATTGCATCCTTCTCTAAGGTCACCAAGATTCTGGCTGCTGCTCTTATGTT
ATTCCTTGGGAAAGACAAAGATGAGAAAAAAGATAGCACCTCAGAATCTGAGGAGGAAGGACCCACAGCAAGAGATCTGC
TTGTGCAATATGCCACAGGGAGGAAGAGCTCCAAAAAATAAGTTAGAAAAGGCAATGAAAGTGCTCAAGAAACAAAAGAA
GAAAAAGCCAGAGGTGTTAGACTTTTCAGCTATTCACTTGATCCATGACCCCCAAGGTCTTGCAGAAAAATGACTCAAGC
AGCAAAAGAACTATAATGAGAGGTCTGAAGTGAAAATGATGCTCATGAACCTTATCTCCAGATTGGTGGGAATCCATGAG
CTTTTTCCTCTTCAATTTCTACCCCTTTTTCCAAAGGTTTCTGCATCCCCACAGAGAGAAATAACAAAGATCCTTCTGTT
TGCTGCACAAGCTTCTCATCACCTTGTACCTCCAGAGATCATTCAATCATTGCTCATGACTGCAGCTAACAAGAACTCTG
GGGAAGTTATGTCAGCAGGTATCAGAATTATAAAGGAAATAACAGCTTGGTGTCCTCTAGCCATGACTGTGGAGCTTTTC
AGGACCTGGCTCAATATAAGAAACACAGAGGTAAAAATGTAATGATGTCTACTAGAACTTTGATCCAGCTCTTCTTGATG
CTGAATCCTCAGACGCTACAGAAGAAATTCTGGGGCAAACCTATGCAAGCTTCTGTAGAAGCAAGAGTACAAGAATTGGT
GAATTAGATGCTAAAGATTATATTCTAGGAGCAGAGTTCTGGAAACTGAGAAAGAAGAGGATGCTGATAATGATGAAGAC
GGGTGGGAAAGTACCAGTCTCAGGGAAGAGGAAGAGGCTGGTGGTGAATGGTTCAAAGGGCACCACTCTTCTGACAAGGA
AAAGCAGATGTCCCAGAAACTGAGCAGCATGACCACGGAGGAGTGCACGGAGGCTGCAGCCATCAGCACCAGTGGGGTCT
GGAAAGAGGACCTCTGGAAAATCCACATGATCCACATGAGGAAAGCGCTTGCCACCGCCCCAGGAAAAGCCCAAAAGAGG
AAATACATTGAAATACAACAGTGCCAAGGAGCCCAAGGGTAAATTATTATCTTTCTGAGACACTGAATGCCTTCATAAAG
AGCCTAATTCTGAGACAATGGAGACATGACTATCAACTGCAATGGCTGGAAAGATAGACCGAAAGGAACTGATGAGGAAG
AACACTAAGGTGAATTCATTTTCCAGTCCATAAATGAAAAGAAGAAAAAAACAGAAGAATATTATGATGATGCAATAGTG
CCAGAATGTTTGGTCCAAAATCAAGCAGTCCTTCCAAGAAAAGCAGGGGACACTACCAGATGCACTTTTGAAGGAGAGA

Alignment

ORF - retro_cpor_510 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.0 %
• Parental protein coverage: 71.41 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  NDAKTVNVITTACFSKVTKILVAALTFFLGKDEDEKKDSDSESEEEGPTARDLLVQYAT-GKKSAKNKKK
          NDAK.VNV...A.FSKVTKIL.AAL..FLGKD.DEKKDS.SESEEEGPTARDLLVQYAT.G....KNK..
Retrocopy NDAKMVNVTMIASFSKVTKILAAALMLFLGKDKDEKKDSTSESEEEGPTARDLLVQYAT>GGRAPKNK--

Parental  LEKAMKVLKKQKKKKKPEVFNFSAIHLIHDPQDFAEKLLRQLENSKERFEVKMMLMNLISRLVGIHELF-
          LEKAMKVLKKQKKKK.PEV..FSAIHLIHDPQ..AEK.L.Q..N..ER.EVKMMLMNLISRLVGIHELF.
Retrocopy LEKAMKVLKKQKKKK-PEVLDFSAIHLIHDPQGLAEK*LKQQKNYNERSEVKMMLMNLISRLVGIHELF>

Parental  LFNFYPFLQRFLQPH-QREVTKILLFAAQASHHLVPPEIIQSLLMTVANNFVTDKNSGEVMTVGINAIKE
          LFNFYPF.QRFL.PH.QRE.TKILLFAAQASHHLVPPEIIQS.L...A.N....KNSGEVM..GI..IKE
Retrocopy LFNFYPFFQRFLHPH<QREITKILLFAAQASHHLVPPEIIQS-LLMTAAN----KNSGEVMSAGIRIIKE

Parental  ITARCPLAMTEELL-QDLAQYKTHKDKNVMMSARTLIQLFRTLNPQMLQKKFRGKPTEASVEARVQEY-G
          ITA.CPLAMT.EL..QDLAQYK.H..KNVMMS.RTLIQLF..LNPQ.LQKKF.GKP..ASVEARVQE..G
Retrocopy ITAWCPLAMTVELF<QDLAQYKKHRGKNVMMSTRTLIQLFLMLNPQTLQKKFWGKPMQASVEARVQEL<G

Parental  ELDAKDYIPGAE-VLEIEKEEDAENDEGDGWESTSLSEEEEADGEWVDVHHSSDEEQQQEISQKLSSMDT
          ELDAKDYI.GAE.VLE.EKEEDA.NDE.DGWESTSL.EEEEA.GEW...HHSSD.E.Q...SQKLSSM.T
Retrocopy ELDAKDYILGAE<VLETEKEEDADNDE-DGWESTSLREEEEAGGEWFKGHHSSDKEKQ--MSQKLSSMTT

Parental  EERKAKAAAVSTSRVLTQEDFQKIRMAQMRKELAAAPGKAQKRKYIEI-DSDEEPRGELLSLRDIERLHK
          EE....AAA.STS.V...ED..KI.M..MRK.LA.APGKAQKRKYIEI..S..EP.G.LLS..D.E.LHK
Retrocopy EEC-TEAAAISTSGVW-KEDLWKIHMIHMRKALATAPGKAQKRKYIEI>NSAKEPKGKLLSF*DTECLHK

Parental  KPKSDK-ETRLATAMAGKTDRKEFVRKKTKMNPFSSSTNKEKKKQKNFMMMRYSQNVRSKTKRSFREKQL
          .P.S...ET.L.TAMAGK.DRKE..RK.TK.N.FSS...K..KKQKN.MMM...QNV.SK.K.SF.EKQ.
Retrocopy EPNSETMET*LSTAMAGKIDRKELMRKNTKVNSFSSP*MKRRKKQKNIMMMQ*CQNVWSKIKQSFQEKQG

Parental  ALRDALLKKR
          .L.DALLK.R
Retrocopy TLPDALLKER

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	20.88 RPM
SRP017611_kidney	0.00 RPM	18.53 RPM
SRP017611_liver	0.00 RPM	13.23 RPM
SRP040447_lung	0.03 RPM	25.98 RPM
SRP040447_skeletal_muscle	0.00 RPM	9.83 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_510 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_510 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008524	2 retrocopies	retro_cpor_510 , retro_cpor_994,
Homo sapiens	ENSG00000198301	2 retrocopies	retro_hsap_2412, retro_hsap_4030,
Gorilla gorilla	ENSGGOG00000006441	1 retrocopy	retro_ggor_1498,
Loxodonta africana	ENSLAFG00000012217	1 retrocopy	retro_lafr_980,
Macaca mulatta	ENSMMUG00000017503	1 retrocopy	retro_mmul_604,
Nomascus leucogenys	ENSNLEG00000027034	1 retrocopy	retro_nleu_2410,
Oryctolagus cuniculus	ENSOCUG00000026953	1 retrocopy	retro_ocun_547,
Pongo abelii	ENSPPYG00000014852	1 retrocopy	retro_pabe_1777,
Pan troglodytes	ENSPTRG00000024399	2 retrocopies	retro_ptro_1388, retro_ptro_2732,
Rattus norvegicus	ENSRNOG00000022229	2 retrocopies	retro_rnor_1381, retro_rnor_1967,
Tupaia belangeri	ENSTBEG00000005270	1 retrocopy	retro_tbel_2414,