RetrogeneDB ID: retro_cpor_1521

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_92:3838550..3839868(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX41
• Ensembl ID: ENSCPOG00000008770
• Aliases: None
• Description: None

Sequence

>retro_cpor_1521
AAGGAAGAGTTAGGCAATGACAGTGAACCCCAGGAAGATGAGGACAGTATCCTGTGGGGCCCTCAGGCTCGTGTCAGCTT
CCTGCATTTGCACCAGCACCTTAAAGAGAAGGCTGCAGCTCACAAGAAGTCTGCAAAAGAGAAGCAATTGAAGGAAAACA
AGACTGGAAAGTGTGATTGAGAGCTGAGCCTTGATGTCAGTGAGGCAGAGGGCCAAGGGCATTACATACAGTGACCAAAT
CAAAGCCAGCTGGACACCTACCAGGAGTATATGTGAAGAGTGGCCCAAGTGCATACCAAAGAAGAACCTCATCTTGGTGC
AAAGAGATGGTATCCCACCACCCACCGAGAGCATCAAGGAAACGAAATTTCCTGCAGCCATCCTGCAAGACCTGAAGAGG
AAAGGCATCCTTTGCCCAATACCCATCCAGATCCCCATCATTATGTCTGGCTGGGACGTGATTGGCATCACCTTCATGGG
GTCAGCCAAGATCCTTGTGTTCATGCTGCCCATCATCATGTCCTGCCCAGAGCAAGCAAAGGGGTTGCCTTTCTCTAAGC
ATGAGGGGTCCTATGGACTATTCGCCCCTTCCATGGCTAGAAGACCTATGGCATCCTGAAATATTACTAACGCCTCCTGC
AGGCTGGGTCATCCTTCTTGCACTGTCCTCTCTGCATTGGGGGCAGATCCAAAGAGCAGATGGAGACCATCCAACATGGT
ATGCACATGATGGTGGCTGCTGCTGGGCACCTTGTAGATTTGGTCATGGAAAGATGGTAAGGCTACACATCTGTCACCAC
CTGGTCCTGGATGAAGTTGACTGCATGATCGACGATGACTTTTAGGGTCACATCTGTATCACCTTCTCCTACTTTAATGG
CCAGCAGCACACACTGCACTTCAGTGCCACCATGCCAAAAAAGATCCAGAACTTTGCCAAGAGTGCCCTGGCAAAGCCTG
TCACTACCAACGTGGAGTCTACAGGGGCTTCCAGCCTGGATGTCATGCAGGAGGAGAACATGTAAAGGAGGAGGCTAAGG
TGGTGCACCTGCTCCTCTGCATACAGAAGACAGCTCTACCCAGGCTCATCTCTGCAGAAAAGAAACCAGACATAGACACC
ATCTGTGACCACCTGCTGCTCAAGAGGGTCAACAATGGCCATCTGTGGGTGCAGAGAGCAGGAAGAGTGGACCAAAGCCA
ATGAAATGTTCCAGGCCAGCAAGAAAGATGTCCTGGTGGTCAAAGACATAGTCTCTAATGGCATGGACTTCCTGCCATCC
AGTACAACATCAATAGTGAAATGCCAGAGGAAACAGAA

Alignment

ORF - retro_cpor_1521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.13 %
• Parental protein coverage: 73.94 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EEQQDCSSEPRGDEDDIPLGPQSNVSLLDQHQHLKEKAEARKESAKEKQLKEEEKI-LESVAEGRALMSV
          .E.....SEP..DED.I..GPQ..VS.L..HQHL..K..A.......K.....E...LESV.E..ALMSV
Retrocopy KEELGNDSEPQEDEDSILWGPQARVSFLHLHQHL--KEKAAAHKKSAKEKQLKENK>LESVIES*ALMSV

Parental  KEMAKGITYDDPIKTSWTPPRYVLSMSEERHERVRKKYHILVEGDGIPPPIKSFKEMKFPAAILRGLKKK
          ...AKGITY.D.IK.SWTP.R...S..EE......KK..ILV..DGIPPP..S.KE.KFPAAIL..LK.K
Retrocopy RQRAKGITYSDQIKASWTPTR---SICEEWPKCIPKKNLILVQRDGIPPPTESIKETKFPAAILQDLKRK

Parental  GILHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQEKRLPFSKREGPYGLIICPSREL
          GIL.P.PIQ...IP.I.SG.D.IGI.F.GS.K.LVF.LP.IM.C.EQ.K.LPFSK.EG.YG....PS...
Retrocopy GILCPIPIQ---IPIIMSGWDVIGITFMGSAKILVFMLPIIMSCPEQAKGLPFSKHEGSYG-LFAPS--M

Parental  ARQ-THGILEYYCRLLQEDSSPLLRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQK-KMVSLDI
          AR..T.GIL.YY.RLLQ..SS..L.C.LCIGG.S.KEQMETI.HG.HMMVA..G.L.DL....KMV.L.I
Retrocopy ARR<TYGILKYY*RLLQAGSS-FLHCPLCIGGRS-KEQMETIQHGMHMMVAAAGHLVDLVME<KMVRLHI

Parental  CRYLALDEADRMIDMGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVGRAGAASLD
          C..L.LDE.D.MID..F.G.I...FSYF.GQ..TL.FSATMPKKIQNFAKSAL.KPVT.NV...GA.SLD
Retrocopy CHHLVLDEVDCMIDDDF*GHICITFSYFNGQQHTLHFSATMPKKIQNFAKSALAKPVTTNVESTGASSLD

Parental  VIQEV-EYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLL-KGVEAVAIHGGKDQEERTKAI
          V.QE..E.VKEEAK.V.LL.C.QKT..P.LI.AEKK.D.D.I...LLL..G....AI.G...QEE.TKA.
Retrocopy VMQEE<EHVKEEAKVVHLLLCIQKTALPRLISAEKKPDIDTICDHLLL>RG-STMAICGCREQEEWTKAN

Parental  EAFREGKKDVLVATDVASKGLDF-PAIQHVINYDMPEEIE
          E.F...KKDVLV..D..S.G.DF.PAIQ..IN..MPEE.E
Retrocopy EMFQASKKDVLVVKDIVSNGMDF<PAIQYNINSEMPEETE

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	0.29 RPM	22.83 RPM
SRP017611_kidney	0.00 RPM	40.20 RPM
SRP017611_liver	0.04 RPM	26.77 RPM
SRP040447_lung	0.23 RPM	50.92 RPM
SRP040447_skeletal_muscle	0.05 RPM	22.94 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1521 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1521 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008770	1 retrocopy	retro_cpor_1521 ,
Loxodonta africana	ENSLAFG00000026418	1 retrocopy	retro_lafr_689,
Macropus eugenii	ENSMEUG00000014375	1 retrocopy	retro_meug_2040,
Otolemur garnettii	ENSOGAG00000011123	1 retrocopy	retro_ogar_1801,
Rattus norvegicus	ENSRNOG00000012771	1 retrocopy	retro_rnor_2396,
Sarcophilus harrisii	ENSSHAG00000014005	1 retrocopy	retro_shar_53,