RetrogeneDB ID: retro_cpor_919

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_34:2260164..2261385(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZC3H15
• Ensembl ID: ENSCPOG00000012965
• Aliases: None
• Description: None

Sequence

>retro_cpor_919
GAAAAAGAAAAGATTATTGAGGACAAAACTCTTGGTCTAAAGAATAAGAAAGGAGCAAAGCAACAGAGTTTATCAAGGCT
GTCACTCATCAAGTTAAATTTGGTCAACAAAATCCTTCTGAGGTAGCACAAAGTGAGACTGAAAAGAAACTGAAGAAAGA
TGACAAGAAAGAATTGCAGGAGCTAAATGGGCTCTTCCGACCTGTCATTGCTGCTCAAAAAAAACCAAGTAAATGTGCAG
ATCTCAAGTCTATGTTGTGTTCCTTCTTCAAGCAGGGGCAGTGCACTGAAGGTGAGAAGTGCAAGTTTTCCATGATCTGA
ACTGGGAGAGAAAATGTGAAAAACGAAGTGTTTACATTGATGCAAGAGATGAAGAACTTGAAAAAGACACCGTGGATAAC
AGGGATAAGAAAAAGCTTGAAGAACTAGTGAATAAGAAGCATGGTGAGGCGGAAAAGAAAAAATCCATACTCAAATAGTC
TACTAGCATTTCCTTGAAGCTATTGAAAATGAAAAGTATGGCTGATTTTGGGTGCGCCCTGGAGAGGGTGATAATTGTAG
GAATCAGCATGCACTTCCTCCTGGATTCGTGTTGAAAAAGATGAAAAGAAAGAAGAGAAAGAAGATGAAATTTAGTTTGA
ACATCTCATTGAAAGAGAGCATTCTGCTGTAGGTCCAAATGTTACCCAAATCACTCTAGAATCTTTTCTTGCGTGGAAGA
AAAGGAAAAGACAAGAAAAGATTGATAAACTTGAACAAGATATGGAAGAAGGAAAGCTGACTTCAAAGCAAGAAAGGCAC
TGATGATCAGTGGTCCAGAAGTGTTTGAATTCCGACCTGAACTGGTCAATGATGATGAGGAGGAAGCTGATGACACACAC
TACACTCAGGGAACAGGTGGTGAGGTGGTGACAAGCTTGAGGATTCCATGAGCATAAATGACATACACGTAAGCCTGTAC
ATCCCAAGAGATGTAGATGAGACAGGCATTACTGTAGCCAGTCTTGAAGGGTTCAGCACACATGCTCCACATAAGGGCGA
AAACAAACTAAGGGAAGCTGGAGGTCGATCTGAAAATGCGGAATGCTGTGACTTGGAAGAGTTCGAGGAAGTGGGTGGAC
TGGAAAACGGAGCCATCAGAGGCGCTTTTGTGGATAAAAATCTTTTCACCAGGAAAGATCTGGATGAATTAGAAGAATTA
AACACATTCGATTAGGAAGAA

Alignment

ORF - retro_cpor_919 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.92 %
• Parental protein coverage: 95.77 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KKEKIIEDKTFGLKNKKGAKQQ-KFIKAVTHQVKFGQQNPRQVAQSEAEKKLKKDDKKKELQELNELFKP
          .KEKIIEDKT.GLKNKKGAKQQ..FIKAVTHQVKFGQQNP..VAQSE.EKKLKKDDKK.ELQELN.LF.P
Retrocopy EKEKIIEDKTLGLKNKKGAKQQ<EFIKAVTHQVKFGQQNPSEVAQSETEKKLKKDDKK-ELQELNGLFRP

Parental  VVAAQKI-SKGADPKSVVCAFFKQGQCTKGDKCKFS-HDLTLERKCEKRSVYIDARDEELEKDTMDNWDE
          V.AA....SK.AD.KS..C.FFKQGQCT.G.KCKFS.HDL..ERKCEKRSVYIDARDEELEKDT.DN.D.
Retrocopy VIAAXXXPSKCADLKSMLCSFFKQGQCTEGEKCKFS<HDLNWERKCEKRSVYIDARDEELEKDTVDNRDK

Parental  KKLEEVVNKKHGEAEKKKP-KTQIVCKHFLEAIENNKYGWFWVCPGGGDNCMYRHALPPGFVLKKDKKKE
          KKLEE.VNKKHGEAEKKK...TQIV..HFLEAIEN.KYG.FWV.PG.GDNC...HALPPGFV........
Retrocopy KKLEELVNKKHGEAEKKKS<HTQIVY*HFLEAIENEKYG*FWVRPGEGDNCRNQHALPPGFVXXXXXXXX

Parental  EKEDEISL-EDLIERERSALGPNVTKITLESFLAWKKRKRQEKIDKLEQDME-RRKADFKAGKALVISGR
          ......SL.E.LIERE.SA.GPNVT.ITLESFLAWKKRKRQEKIDKLEQDME.RRKADFKA.KAL.ISG.
Retrocopy XXXXXFSL<EHLIEREHSAVGPNVTQITLESFLAWKKRKRQEKIDKLEQDME<RRKADFKARKALMISGP

Parental  EVFEFRPELVN-DDDEEADD--TRYTQGA-GGDEVDDSMSVNDIDLSLYIPRDVDETGITVASLERFSIY
          EVFEFRPELVN.D..E..D...T..T.G..GGD...DSMS.NDI..SLYIPRDVDETGITVASLE.FS..
Retrocopy EVFEFRPELVNDDEEEADDTHYTQGTGGE<GGDKLEDSMSINDIHVSLYIPRDVDETGITVASLEGFSTH

Parental  APDKDENKLSEASGGRAENGERSDLEEGSEAGGPENGALGAVPVDENLFTGEDLDELEEELNTLDLEE
          AP.K.ENKL.EA.GGR.EN.E..DLEE..E.GG.ENGA.....VD.NLFT..DLDEL.EELNT.D.EE
Retrocopy APHKGENKLREA-GGRSENAECCDLEEFEEVGGLENGAIRGAFVDKNLFTRKDLDEL-EELNTFD*EE

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	52.40 RPM
SRP017611_kidney	0.00 RPM	48.68 RPM
SRP017611_liver	0.00 RPM	32.12 RPM
SRP040447_lung	0.00 RPM	31.95 RPM
SRP040447_skeletal_muscle	0.01 RPM	22.17 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_919 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_919 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 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021762	1 retrocopy	retro_btau_1223,
Choloepus hoffmanni	ENSCHOG00000011958	1 retrocopy	retro_chof_2120,
Callithrix jacchus	ENSCJAG00000005931	2 retrocopies	retro_cjac_2883, retro_cjac_3986,
Cavia porcellus	ENSCPOG00000012965	2 retrocopies	retro_cpor_1294, retro_cpor_919 ,
Dipodomys ordii	ENSDORG00000011664	1 retrocopy	retro_dord_666,
Loxodonta africana	ENSLAFG00000001563	1 retrocopy	retro_lafr_941,
Myotis lucifugus	ENSMLUG00000007741	2 retrocopies	retro_mluc_1494, retro_mluc_2467,
Monodelphis domestica	ENSMODG00000027565	5 retrocopies	retro_mdom_1230, retro_mdom_1321, retro_mdom_1744, retro_mdom_1942, retro_mdom_871,
Oryctolagus cuniculus	ENSOCUG00000011903	1 retrocopy	retro_ocun_886,
Otolemur garnettii	ENSOGAG00000002182	2 retrocopies	retro_ogar_1093, retro_ogar_611,
Ochotona princeps	ENSOPRG00000015790	2 retrocopies	retro_opri_169, retro_opri_609,
Pan troglodytes	ENSPTRG00000012717	1 retrocopy	retro_ptro_348,
Rattus norvegicus	ENSRNOG00000005256	4 retrocopies	retro_rnor_2628, retro_rnor_284, retro_rnor_662, retro_rnor_925,
Sorex araneus	ENSSARG00000012071	1 retrocopy	retro_sara_363,