RetrogeneDB ID: retro_cpor_727

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_25:2271136..2272489(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000026514
• Aliases: None
• Description: None

Sequence

>retro_cpor_727
AGCCAACTGGTCACGCAGCCTTGTGTGATGGAGTGGGCAGACACTGTGAGTCTTTTGACCCTTCTTTGGATTTCATGGAG
AACTTTTTGTTCTGTTAGAAGTTGGTTGGCAGTGAGCAGAGAAAAAGGGCTCGCTCTCCAGCTCGCAGGACTCCTTAAAG
AAAAGTACCAACTCTTGGACCAACTCGGCCAGCTTCAGAAAGAACAGGAAGCCTTAGAGACAACTCTCAAGGAGGTCGGC
CCAGAAGAGGAGGCCAGGGCAGCACAGCGTTGGAAGGCAGCCAAAGAGAAGGTGTTGCTGTTGAGGAACAGATCGAAGAT
TCGAGGGCAGGTAGACCGCCTCCTCAAAGAGCAAAAAGAGCATGTTCGACAACAGCAATCAGAGATGGCAGAGACAGCAA
ACAGGATCGGGTCCCTGGCAGAGGAATTAACATCAGTGACTTCGGAAATAGCTAACATGAAATTCGCCTTGTGGAACATG
GGCAAAGAGCGGCTCCAGAGAGAAATGACAGTTGCTCTGAGTGAGAATGCCCAACTCCCCGAAAGCCACTCACAGCTTTC
CCAGGAAGCTCAACGGGGAAGGGAACGAGGGGCTGAAGTCATGAGTCAACTGGAAAATGGTCCTGTCTCAGGTCATCAGC
CAAGAGTGTCTTTGGAGAAACCAGTGTATGGTGCTCAATTAAATGCGTCCTTAAAGACCACGGAAGAGCAAAGAAACCAA
CTTTGCACTCAACTCTGGGAGGCAGAGAACACTGAGAAAGAACTGAAAAAGTCTCTGTATAGTCTCCAGACTCAGAAAAC
ATCTCTGGAGTCAGCCAAGGCACAGCTGCAAGGCGAGCACCAGAAGCTTGAGCAGAAGGTCACAGTGATGGGTGAGGTTC
ACCACCAAACTGTGCCGCGAAGCCACACCAAACTGAGACAGCAGGCCAGAGTCCGGGCAGAGCAAGGAAGGAAACTGCCC
ATATGGGAAGAGGAGGTGGGCCACACTGCTCAAGAGCTGGAGACCTACAGGAAGATAGCCCAGGACATGCAGGAGGAGTG
GGAGAAAACCATTCGCTCCCACCAAAGGCAGCTGACCTGCATGCAGAAGGAAGCCCACAAGAACTGGGCTGCAGCTGCCA
CTGCTGGAAGCCTGCTCCGGGAGTTAAGGAGGGGAAATGCTCGCACCAAAGAGATCCTGCGTGCCATGGAGATGAAGGCT
TCCCACTTGGGCCAAGATCCTGACACCCATGGCGTGATGAAGAGCTCAGCTGGAAGACAGCATTGCCTGCGTGGTCCTTC
CCGTCGAGGGAGGCCAGGCCAAGGAAGGAAATCTGCTCACCTTAGTCTTCCAACGCTGTGGGAGGAGCCGCTG

Alignment

ORF - retro_cpor_727 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQLVTQPCVMEWADTMSLLTLLWISWRTFRCVRSRLAVSREKPLALQLTGLLKEKCQLLDQLDQLQKEHE
          SQLVTQPCVMEWADT.SLLTLLWISWRTF..VRS.LAVSREK.LALQL.GLLKEK.QLLDQL.QLQKE.E
Retrocopy SQLVTQPCVMEWADTVSLLTLLWISWRTFCSVRSWLAVSREKGLALQLAGLLKEKYQLLDQLGQLQKEQE

Parental  ALETALKEVRLEEEARAAQCLEATKKKVLMLWNRSKIVGQIDRLLKERKEEQAERVRKQQSEMAETANRI
          ALET.LKEV..EEEARAAQ...A.K.KVL.L.NRSKI.GQ.DRLLK....EQ.E.VR.QQSEMAETANRI
Retrocopy ALETTLKEVGPEEEARAAQRWKAAKEKVLLLRNRSKIRGQVDRLLK----EQKEHVRQQQSEMAETANRI

Parental  GSLAEELTSVTPEIANMKLALRNMGIQQLQREMTVALSENAQLPESHSQLSQEAQRGKERGAEVKSQQEN
          GSLAEELTSVT.EIANMK.AL.NMG...LQREMTVALSENAQLPESHSQLSQEAQRG.ERGAEV.SQ.EN
Retrocopy GSLAEELTSVTSEIANMKFALWNMGKERLQREMTVALSENAQLPESHSQLSQEAQRGRERGAEVMSQLEN

Parental  GPGSGHQPRVLLEKPVYGARLNASLKTTEEQRNQLRTQLWEAENTEKELKKSLYRLQTKKASLESAKAQL
          GP.SGHQPRV.LEKPVYGA.LNASLKTTEEQRNQL.TQLWEAENTEKELKKSLY.LQT.K.SLESAKAQL
Retrocopy GPVSGHQPRVSLEKPVYGAQLNASLKTTEEQRNQLCTQLWEAENTEKELKKSLYSLQTQKTSLESAKAQL

Parental  QGEHQKLQQKFRGMGQIHHQAVLRCHTKLRQQARVGAEQGRKLPIREEEVGHSAQELETYRKIAQDMQEE
          QGEHQKL.QK...MG..HHQ.V.R.HTKLRQQARV.AEQGRKLPI.EEEVGH.AQELETYRKIAQDMQEE
Retrocopy QGEHQKLEQKVTVMGEVHHQTVPRSHTKLRQQARVRAEQGRKLPIWEEEVGHTAQELETYRKIAQDMQEE

Parental  WEKTIRSHQRQLTCMQKEARKNWAAAATAGSLLRELRRGNARTKEILRAMEKKASHLGQDPDTHGVMKSS
          WEKTIRSHQRQLTCMQKEA.KNWAAAATAGSLLRELRRGNARTKEILRAME.KASHLGQDPDTHGVMKSS
Retrocopy WEKTIRSHQRQLTCMQKEAHKNWAAAATAGSLLRELRRGNARTKEILRAMEMKASHLGQDPDTHGVMKSS

Parental  AGRQHCLRGPSRRSRPGRGRRSAHLSLPMLWEEPL
          AGRQHCLRGPSRR.RPG.GR.SAHLSLP.LWEEPL
Retrocopy AGRQHCLRGPSRRGRPGQGRKSAHLSLPTLWEEPL

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	0.06 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP040447_lung	0.03 RPM	0.00 RPM
SRP040447_skeletal_muscle	0.03 RPM	0.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_727 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_727 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 9 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016105	4 retrocopies	retro_cjac_1747, retro_cjac_2711, retro_cjac_3217, retro_cjac_921,
Cavia porcellus	ENSCPOG00000026514	2 retrocopies	retro_cpor_189, retro_cpor_727 ,
Homo sapiens	ENSG00000150527	3 retrocopies	retro_hsap_1201, retro_hsap_3691, retro_hsap_640,
Homo sapiens	ENSG00000258941	1 retrocopy	retro_hsap_78,
Gorilla gorilla	ENSGGOG00000011990	1 retrocopy	retro_ggor_936,
Nomascus leucogenys	ENSNLEG00000004121	10 retrocopies	retro_nleu_1218, retro_nleu_1690, retro_nleu_2087, retro_nleu_2103, retro_nleu_2148, retro_nleu_2600, retro_nleu_2951, retro_nleu_3017, retro_nleu_3077, retro_nleu_688,
Pongo abelii	ENSPPYG00000005768	9 retrocopies	retro_pabe_1001, retro_pabe_1002, retro_pabe_1007, retro_pabe_1055, retro_pabe_1060, retro_pabe_1588, retro_pabe_2119, retro_pabe_29, retro_pabe_3024,
Pan troglodytes	ENSPTRG00000006297	10 retrocopies	retro_ptro_1286, retro_ptro_1712, retro_ptro_2503, retro_ptro_2580, retro_ptro_2880, retro_ptro_466, retro_ptro_821, retro_ptro_826, retro_ptro_868, retro_ptro_876,
Ictidomys tridecemlineatus	ENSSTOG00000015890	1 retrocopy	retro_itri_95,