RetrogeneDB ID: retro_cjac_2484

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:146200665..146201844(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF131
• Ensembl ID: ENSCJAG00000001280
• Aliases: None
• Description: None

Sequence

>retro_cjac_2484
ATGAAAGCCCTTGAAGTCAGGAACAAAGAAAACTCAGCTCCATTAGAGGAAAATACCACAGGAAAAAGTGAGGCCAAAAA
CAAGGAAGATTGCAGAAACTTCAAATGTTACTACAGAATCATTGCCATCTGCAGAATCAGAACCTATTGAAATTGAGGTA
GAGATTGCTGACGGCACAATTGAAGTGGAAGATGAAGGCATCAAAACATTAGAGGTAGTGGATTCTGCCAAGGGTCGATA
ACGTACATACAGAGCACGGGTTCCTCTAATGATTTTGCTGTAGCACTCTCGGCAGATATTACCAGCAAGTGCCATCAAGG
TGACAGAAAAGGGCAGATTAAAGAAAAAGATGGCTTTGCATCTGACCCCACAAGCATAGAGATAGAAAGTACTGACATTG
TGGAACTTTAGTTGTCCTATGTGAAGGACTTGCTCCATTGTGAGAAATGCAATGGTTCATTTAAATTGTTTTATCATTTG
AAGGAACACACGAAATCCCACTCTCCTGAGAGTTTCAAGTGTGAAACGTGCAATAAAAGATATCTTTGGGAGAGCACATG
AAAACAGCACCTGAATTGTTACCATCTTGAAGAAGGTGGAGTCACTAAGAAGCAAAGAACTGGGAAAAAAGTTTATGTAT
GTCAATACTGTGAGAAGCAGTTTGACGGTTTTGGATATTTTAAAGAACACCTTTGAAAACAAACAGGTGAAAAACCTTTT
TAGTGTCCAAATTGTGATAAAAGATTTGCTAGAAATAGCACCTTCAAATGTCATCTCACTGCATGCCAAACTGGAGTAGC
GGCAAAAAAAGAAAAAAGAAGCTCTATGAATGCCAGGTCTGCAACAGTGTGTTTAACAGCTGGGACCAGTTCAAAGACCA
CTTGGTAATACACACTGGATGTAAACCCAACCACTGTTCTTTATGTGACTTGTGGTTTATTCAAGAAAATAAATTAATGA
GACATCTCAATGATACTCACAATATTTCAGAGCATCTAGTATTGGAAGAAGTTATTTCAGTAGAAACACATTTGCAAACT
GAACCTGTGACATCAATGACTATTACAGAACAAGTTGGGAAGGTGCATGTGCTACCATTGCTTCAGGTCCAGGTTGGATT
CAGCACAAATGACTAGGGAACATGTCCATCCAGATCTTCTCCAGGACCTCCAGATACAT

Alignment

ORF - retro_cjac_2484 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.11 %
• Parental protein coverage: 62.92 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IKALEVRNKENSAPLEENTTGKSEAKK-RKIAETSNVITESLPSAESEPVEIEVEIAEGTIEVEDEGVET
          .KALEVRNKENSAPLEENTTGKSEAK..RKIAETSNV.TESLPSAESEP.EIEVEIA.GTIEVEDEG..T
Retrocopy MKALEVRNKENSAPLEENTTGKSEAKN>RKIAETSNVTTESLPSAESEPIEIEVEIADGTIEVEDEGIKT

Parental  LEEVASAKQ-SIKYIQSTGSSDDSALALLADITSKYRQGDRKGQIKEDD-CASDPTSKQVEGIEIVELQL
          LE.V.SAK..SI.YIQSTGSS.D.A.AL.ADITSK..QGDRKGQIKE.D..ASDPTS...E...IVEL.L
Retrocopy LEVVDSAKG<SITYIQSTGSSNDFAVALSADITSKCHQGDRKGQIKEKDGFASDPTSIEIESTDIVEL*L

Parental  SHVKDLFHCEKCNRSFKLFYHFKEHMKSHSTESFKCEICNKRYLRESAWKQHLNCYHLEEGGVSKKQRTG
          S.VKDL.HCEKCN.SFKLFYH.KEH.KSHS.ESFKCE.CNKRYL.ES..KQHLNCYHLEEGGV.KKQRTG
Retrocopy SYVKDLLHCEKCNGSFKLFYHLKEHTKSHSPESFKCETCNKRYLWEST*KQHLNCYHLEEGGVTKKQRTG

Parental  KKIHVCQYCEKQFDHFGHFKEHLRKHTGEKPFECPNCHERFARNSTLKCHLTACQTGVGA-KKGRKKLYE
          KK..VCQYCEKQFD.FG.FKEHL.K.TGEKPF.CPNC..RFARNST.KCHLTACQTGV.A.KK..KKLYE
Retrocopy KKVYVCQYCEKQFDGFGYFKEHL*KQTGEKPF*CPNCDKRFARNSTFKCHLTACQTGVAA<KKRKKKLYE

Parental  CQVCNSVFNSWDQFKDHLVIHTGDKPNHCTLCDLWFMQGNELRRHLSDAHNISERLVTEEFLSVETRVQT
          CQVCNSVFNSWDQFKDHLVIHTG.KPNHC.LCDLWF.Q.N.L.RHL.D.HNISE.LV.EE..SVET..QT
Retrocopy CQVCNSVFNSWDQFKDHLVIHTGCKPNHCSLCDLWFIQENKLMRHLNDTHNISEHLVLEEVISVETHLQT

Parental  EPVTSMTIIEQVGKVHVLPLLQVQV-DSAQVTVEQVHPDLLQDNQVH
          EPVTSMTI.EQVGKVHVLPLLQVQV.DSAQ.T.E.VHPDLLQD.Q.H
Retrocopy EPVTSMTITEQVGKVHVLPLLQVQV>DSAQMTREHVHPDLLQDLQIH

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
SRP051959_colon	0.02 RPM	9.52 RPM
SRP051959_heart	0.30 RPM	9.56 RPM
SRP051959_kidney	0.20 RPM	9.54 RPM
SRP051959_liver	0.06 RPM	10.53 RPM
SRP051959_lung	0.21 RPM	13.26 RPM
SRP051959_lymph_node	0.25 RPM	16.67 RPM
SRP051959_skeletal_muscle	1.05 RPM	9.22 RPM
SRP051959_spleen	0.38 RPM	13.07 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2484 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2484 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2484 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001280	1 retrocopy	retro_cjac_2484 ,
Cavia porcellus	ENSCPOG00000011858	1 retrocopy	retro_cpor_350,
Echinops telfairi	ENSETEG00000015357	1 retrocopy	retro_etel_1596,
Gorilla gorilla	ENSGGOG00000002252	1 retrocopy	retro_ggor_2485,
Ictidomys tridecemlineatus	ENSSTOG00000015383	1 retrocopy	retro_itri_1485,
Tursiops truncatus	ENSTTRG00000009644	1 retrocopy	retro_ttru_418,