RetrogeneDB ID: retro_cpor_587

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_2:50967082..50968555(+)
• Located in intron of: ENSCPOG00000023473

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000011295
• Aliases: None
• Description: None

Sequence

>retro_cpor_587
GTGACCCTGTCTCTGGTCTTTGCCATCAGTATTGCTGCAATTGGCTCTTTCCAGTTTGGCTACAACACTGGAGTCATCAA
TGCTCCTGAGACGATCATAAGAGACTTTCTCAACTACACCTTGTCAGAGAAGTTAGGTAAGCCTCCCAGTAAAGGGCTGC
TTACAACCCTCTGGTCCTTGTCTGTGGCCATCTTCTCTGTGGGTGGAATGCTTGGCTCCTTTTCCATTGGACTCTTTGTC
AACCGCTTTGGCAGGCGCAGTTCAATGCTCATGGTCAACCTTTTGGCCATCACTGGTGGCTTCCTTATGGGTTTTTGCAA
GATGGCTGAGTCTGTGGAGATGCTGATACTGGGCCGCTTGGTCATTGGTGTCTTCTGTGGACTCTGCACAGGTTTTGTGC
CCATGTACATTGGAGAGGTGTCTCCCACTGCTTTTCGGGGTGCCTTCGGCACCCTCCACCAGCTAGCCATCGTCATCGGG
ATTCTGGTGGCTCAGATCTTTGGCTTAAGATCCATCTTGGGTACTGAAAGGGACTGGCCTGTGCTGTTGGGCCTTCCCAT
CATTCCAGCCGTCTTACAAAGTGTAGCCCTTCCGTTTTGCCCTGAGAGTCCAAGATTCTTGCTCTTTAACAGAAAGGAAG
AGGCGAATGCTACAGAGATCCTCCGGCAGCTGTGGGGCACCCTGGATGTGTCCCGGAGCATCCAGGAGATGAAAGAGGAG
AGTGTTAGGATGAGCCAGGAAAAGAAAGTCACTGTGCTGGAGCTCTTTAGGTCCCGCAGCTACCAACAGCCCATTATCAT
CTCCATTGTGCTCCAGCTATCCCAGCAGCTCTCTGGGATCAATGCTGTATTCTATTACTCAACAGGAATCTTCCAGGATG
CAGATGTGCAGGAGCCAATCTATGCCACCATCGGAGCAGGTGTGGTCAATACTGTCTTCACTATGGTTTCTCTGTTTCTG
GTGGAAAGAGCAGGACGGAAGAGTCTGCATATGATTGGCCTCGGAGGGATGGCTGTTTGTTCCATCTTCATGATGATCTC
TCTGTTACTGAAGGACACATACGGTTTCATGAGCTACATCTGCATCATGGCTATCTTGATCTACGTGGCCTTCTTTGAGA
TTGGACCTGGGCCCATTCCCTGGTTTATTGTGGCTGAACTCTTCAGCCAGGGACCCCGCCCGGCTGCCATGGCCATAGCT
GGGTGTTCTAACTGGACTTCCAACTTTTTGGTTGCACTGCTCTTCCCCTTGGCTGTGGCCTCTTTAGGCGCCTACGTTTT
TATCATCTTCACCATTTTCCTCATTATATTCTTACTGTTCACCTTCTTCAAAGTCCCTGAAACCCGAGGCAGGACTTTTG
AGGACATCAGACGGGTCTTTGAAGAGTACGCTCAGGAAGGCCCAGAATCTGAGAAGAGCCCCGCCGTGGAGCTGAACAGG
CTGCAGCCAGAGAAGGAAATGGCCTCTGGCATC

Alignment

ORF - retro_cpor_587 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTPSLVFAITIAAIGSFQFGYNTGVINAPEMIITEFINSTLSQKLGNPPSKELLTTLWSLSVAIFSVGGM
          VT.SLVFAI.IAAIGSFQFGYNTGVINAPE.II..F.N.TLS.KLG.PPSK.LLTTLWSLSVAIFSVGGM
Retrocopy VTLSLVFAISIAAIGSFQFGYNTGVINAPETIIRDFLNYTLSEKLGKPPSKGLLTTLWSLSVAIFSVGGM

Parental  LGSFSVGLFVNRFGRRNSMLMVNVLVVVSGCLMGFCKMAKSVEMLILGRLITGIFCGLCTGFVPMYIGEV
          LGSFS.GLFVNRFGRR.SMLMVN.L....G.LMGFCKMA.SVEMLILGRL..G.FCGLCTGFVPMYIGEV
Retrocopy LGSFSIGLFVNRFGRRSSMLMVNLLAITGGFLMGFCKMAESVEMLILGRLVIGVFCGLCTGFVPMYIGEV

Parental  SPTNLRGAFGALHQLGIVIGILVAQIFGLKFILGTEEHWPLLLAFTILPAILQSIALPFCPKSPRFLLIN
          SPT..RGAFG.LHQL.IVIGILVAQIFGL..ILGTE..WP.LL...I.PA.LQS.ALPFCP.SPRFLL.N
Retrocopy SPTAFRGAFGTLHQLAIVIGILVAQIFGLRSILGTERDWPVLLGLPIIPAVLQSVALPFCPESPRFLLFN

Parental  RKEEESATKILQRLWGAQDVSQDIQEMKDESVRMSQEKKATVLELFRSHKYQQPIMIAIMLQLSQQLSGI
          RKEE..AT.IL..LWG..DVS..IQEMK.ESVRMSQEKK.TVLELFRS..YQQPI.I.I.LQLSQQLSGI
Retrocopy RKEEANATEILRQLWGTLDVSRSIQEMKEESVRMSQEKKVTVLELFRSRSYQQPIIISIVLQLSQQLSGI

Parental  NAVFYYSTGIFEDAGVQEPIYATIGAGVVNTIFTVVSVFLVDRAGRRSLHLIGLGGMAVCSIIMTISLLL
          NAVFYYSTGIF.DA.VQEPIYATIGAGVVNT.FT.VS.FLV.RAGR.SLH.IGLGGMAVCSI.M.ISLLL
Retrocopy NAVFYYSTGIFQDADVQEPIYATIGAGVVNTVFTMVSLFLVERAGRKSLHMIGLGGMAVCSIFMMISLLL

Parental  KSSYGFMSYICIVAILIYVAFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGCSNWTSNFLVGLLFPLAAA
          K..YGFMSYICI.AILIYVAFFEIGPGPIPWFIVAELFSQGPRPAAMA.AGCSNWTSNFLV.LLFPLA.A
Retrocopy KDTYGFMSYICIMAILIYVAFFEIGPGPIPWFIVAELFSQGPRPAAMAIAGCSNWTSNFLVALLFPLAVA

Parental  ALGAYVFIIFAVFLIIFLLFTFFKVPETRGRTFEEITRAFEGHADDAQEPGKSSALELNSLQPEKEPVAG
          .LGAYVFIIF..FLIIFLLFTFFKVPETRGRTFE.I.R.FE..A....E..KS.A.ELN.LQPEKE...G
Retrocopy SLGAYVFIIFTIFLIIFLLFTFFKVPETRGRTFEDIRRVFEEYAQEGPESEKSPAVELNRLQPEKEMASG

Parental  V
          .
Retrocopy I

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	39.80 RPM
SRP017611_kidney	0.10 RPM	2.62 RPM
SRP017611_liver	0.13 RPM	1.57 RPM
SRP040447_lung	0.05 RPM	37.91 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_587 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_587 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004556	2 retrocopies	retro_btau_708, retro_btau_709,
Callithrix jacchus	ENSCJAG00000018988	1 retrocopy	retro_cjac_446,
Cavia porcellus	ENSCPOG00000003074	1 retrocopy	retro_cpor_761,
Cavia porcellus	ENSCPOG00000009834	1 retrocopy	retro_cpor_760,
Cavia porcellus	ENSCPOG00000011295	1 retrocopy	retro_cpor_587 ,
Felis catus	ENSFCAG00000001625	1 retrocopy	retro_fcat_1924,
Homo sapiens	ENSG00000059804	2 retrocopies	retro_hsap_3983, retro_hsap_401,
Gorilla gorilla	ENSGGOG00000016813	1 retrocopy	retro_ggor_398,
Macaca mulatta	ENSMMUG00000000439	2 retrocopies	retro_mmul_2301, retro_mmul_502,
Nomascus leucogenys	ENSNLEG00000026903	2 retrocopies	retro_nleu_1572, retro_nleu_1904,
Oryctolagus cuniculus	ENSOCUG00000008575	1 retrocopy	retro_ocun_352,
Pongo abelii	ENSPPYG00000004234	1 retrocopy	retro_pabe_3274,
Pongo abelii	ENSPPYG00000004235	1 retrocopy	retro_pabe_315,
Pan troglodytes	ENSPTRG00000004624	1 retrocopy	retro_ptro_2703,
Pan troglodytes	ENSPTRG00000004626	1 retrocopy	retro_ptro_307,