RetrogeneDB ID: retro_cjac_2142

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:58844129..58847381(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000003236
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KIF4A
• Ensembl ID: ENSCJAG00000015566
• Aliases: None
• Description: None

Sequence

>retro_cjac_2142
ATGAAGGAAGAGGTGAAGGGAATTCCTGTAAGAGTGGCGCTGCGTTGTCGCCCTCTGGTCCCCAAAGAGATTAGCGAGGG
CTGCCAGATGTGCCTTTCCTTCGTGCCCGGGGAGCCTCAGGTGGTGGTTGGTACTGATAAGTCCTTCACCTACGATTTTG
TGTTTGATCCTTCTACTGAACAGGAAGAAGTCTTCAATACAGCAGTAGCGCCGCTCATAAAAGGCGTATTTAAAGGATAT
AATGCAACCGTCCTGGCCTATGGGCAGACTGGCTCTGGAAAAACCTATTCGATGGGAGGTGCATACACTGCAGAGCAAGA
GAATGAACCGACAGTAGGGGTTATTCCTAGGGTAATACAACTGCTCTTCAAAGAAATTGATAAAAAGAGTGACTTTGAAT
TTATTTTGAAAGTGTCTTACTTAGAGATTTACAATGAAGAAATTTTGGATCTTCTACGCCCATCTCATGAGAAATCTCAA
ATAAATATACGGGAGGATCCTAAGGAAGGCATAAAGATTGTGGGACTCACTGAGAAGACTGTTTTAGTTGCCTTGGATAC
TGTTTCCTGTTTGGAGCAGGGCAACAACTGTAGGACTGTAGCCTCCACAGCTATGAACTCCCAGTCATCCCGATCTCATG
CCATCTTTACAATCTCCATAGAGCAAAGAAAGAAAAGTGACAAGAATAGTAGCTTTCACTCCAAGCTGCATCTTGTAGAC
CTCTCTGGATCAGAAAGACAGAAGAAAACCAAGGCTGAAGGGGATCGTCTGAAAGAGGGTATTTATATTAACCGAGGCCT
CCTATGCTTGGGAAATGTAATCAGCGCTCTTGGAGATGACAAAAAGGGTGGATTTGTGCCCTACAGAGATTCCAAGTTGA
CTCGACTGCTTCAAGATTCTCTGGGAGGTAACAGTCATACTCTTATGATAGCCTGTGTGAGTCCTGCTGACTCCAATCTA
GAAGAAACATTAAATACCCTTCGCTATGCTGACAGAGCAAGAAAAATCAAGAACAAACCTATTGTTAATATTGATCCCCA
GACAGCTGAACTTAATCATCTAAAGCAACAGGTACAACAGCTGCAGGTCTTGCTGCTACAAGCCCGTGGAAGTACCCTGC
CTGGATCTATAAATATGGAACCATCAGAGAATCTGCAGTCCCTGATGGAGAAGAATCAGTCCCTGGTAGAGGAGAATGAA
AAATTAAGTCGTGGTCTGAGTGAGGCAGCTGGTCAGACAGCCCAGATGTTGGAGAGGATCATTTTGACAGAACAAGCAAA
TGAAAAAATGAGCGCCAAGCTAGAAGAGCTCAGGCACCATGCAGCCTGCAAACTGAATCTTCAAAAGCTAGTGGAGACTT
TGGAAGATGAGGAATTGAAAGAAAATGTAGAGATAATTTGTAACCTGCAGCAATTGATTACCCAGTTATCGGATGAAACT
GTTGCTTGCATGGTTGCAGCCATTGACACGGTAGTGGAACAAGAAGCCCAAGTGGAAACCAGTCCAGAGATGAGCAGGTC
TTCTGATGGTTTTACCACTCAGCATGCTCTCCGTCAAGCACAGATGTCTAAGGAGCTGATTGAGTTGAATAAAGCCCTTG
CACTGAAAGAGGCCCTGGCTAGGAAGATGACTCAGAATGACAGCCAACTACAGCCCATTCAATTCCAATACCAGGATAAC
ATAAAAGGTCTAGAATTAGAAGTCATCAATCTGCAAAAGGAAAAGGAAGAATTGGTTCTTGAAGTTCAGACTGCAAAGAA
GGATGTCAACCAAGCCAAGTTGAGTGAGCACCGCCGCAAACGTCTCCAGGAGCTGGAGGGTCAAATTGCTGATCTGAAGA
AGAAACTGAATGAGCAGTCCAAACTTCTGAAACTAAAGGAATCCACAGAGCATACTGTCACCAAACTTAACCAGGAGATA
CGGATGATGAAAAACCAGCGGGTACAGTTAATGCGTCAAATGAAAGAGGATGCTGAGAAGTTCAGACAGTGGAAGCAGAA
AAAAGACAAAGAAGTAATACAGTTAAAAGAAAGAGACCGTAAGAGGCAATATGAGCTGCTGAAACTTGAAAGAAACCTCC
AGAAACAATCCAATGTGCTCAGACGTAAAACAGAGGAGGCAGCAGCTGCCAATAAGCGTCTCAAGGATGCTCTCCAGAAA
CAACAGGAGGTCGTGGATAAGCGGAAAGAGACTCAGAGCCGTGGAATGGAAAGCACTGCAGCTCGAGTGAAGACTTGGCT
TGGAAATGAGATTGAGGTTATGGTTAGTACTGAGGAAGCCAGACGCCATCTGAATGACCTCCTTGAAGACAGAAAGATCC
TGGCTCAAGATGTGGCTCAACTCAAAAAAAAAAAGGAATCTGGGGAGAATCCACCCCCTAAACTCCGGAGGTGTACTTTC
TCCCTTACTGAAGGGCATGCTCAAGTTTCAGAGTCAGAAGATTCTATTACAAAGCAGATTGAAAGCCTAGAGACTGAAAT
GGAGTTCAGGAATGCTCAGATTGCTGACCTACAGCAGAAGCTGATAGATGCAGAAAGTGAGGACAGACCAAAACAACGCT
GGGAGAATATTGCCACCATTGTGGAAGCCAAGTGTGCCCTGAAATATTTGATTGGAGAGCTGGTCTCCTCCAAAATACAA
GTCATCAAACTTGAAAGCAGCCTGAAACAGAGCAAGGCCAGCTGTGCTGACATGAAGAAGACGCTGTTTGAGGAACAAAA
TCATTTTGCCCAGATAGAGACAGAGTTACAAGCTGAGCTGGTCAGAATGGAGCAACAGCACCAGGAGAAGGTGCTGTACC
TTCTCGGGCAGCTGCAGCAAAGTCAAATGGCAGAGAAACAGTTAGAGGAATCAATCAGTGAAAAGGAACAGCAGCAGCTG
AGCACACTGAAGTGTCAGGATGAACTTGATAAGATGCGAGAAGTGTGTGAGCAAAATCAGCAGCTTCTCCGAGAGAATGA
AATCATCAAGCAGAAACTGACCCTCCTCCAGGTATCCAGCAGACAGAAACCTCTTCCTAAGGATGCCCTTCTATCTCCAG
ATTCTTCTTTTGAATATATCCCACCTAAGCCAAAACCTTCTCGTGTTAAAGAAAAGTTCCTGGAGCAGAGCATGGACATT
GAGGATCTAAAATATTGTTCAGAGCATTCTGTCAATGAGCATGAGGATGGTGATGGTGACAGTGATGAGGGTGATGATGA
GGAATGGAAGCCAACAAAATTAGTTAAGGTGTCCAGGAAGAACGTCCAAGGG

Alignment

ORF - retro_cjac_2142 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.19 %
• Parental protein coverage: 99.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKEEVKGIPVRVALRCRPLVPKEISEGCQMCLSFVPGEPQVVVGTDKSFTYDFVFDPSTEQEEVFNTAVA
          MKEEVKGIPVRVALRCRPLVPKEISEGCQMCLSFVPGEPQVVVGTDKSFTYDFVFDPSTEQEEVFNTAVA
Retrocopy MKEEVKGIPVRVALRCRPLVPKEISEGCQMCLSFVPGEPQVVVGTDKSFTYDFVFDPSTEQEEVFNTAVA

Parental  PLIKGVFKGYNATVLAYGQTGSGKTYSMGGAYTAEQENEPTVGVIPRVIQLLFKEIDKKSDIEFTLKVSY
          PLIKGVFKGYNATVLAYGQTGSGKTYSMGGAYTAEQENEPTVGVIPRVIQLLFKEIDKKSD.EF.LKVSY
Retrocopy PLIKGVFKGYNATVLAYGQTGSGKTYSMGGAYTAEQENEPTVGVIPRVIQLLFKEIDKKSDFEFILKVSY

Parental  LEIYNEEILDLLCPSREKSQINIREDPKEGIKIVGLTEKTVLVALDTVSCLEQGNNSRTVASTAMNSQSS
          LEIYNEEILDLL.PS.EKSQINIREDPKEGIKIVGLTEKTVLVALDTVSCLEQGNN.RTVASTAMNSQSS
Retrocopy LEIYNEEILDLLRPSHEKSQINIREDPKEGIKIVGLTEKTVLVALDTVSCLEQGNNCRTVASTAMNSQSS

Parental  RSHAIFTISIEQRKKSDKNSSFHSKLHLVDLAGSERQKKTKAEGDRLKEGININRGLLCLGNVISALGDD
          RSHAIFTISIEQRKKSDKNSSFHSKLHLVDL.GSERQKKTKAEGDRLKEGI.INRGLLCLGNVISALGDD
Retrocopy RSHAIFTISIEQRKKSDKNSSFHSKLHLVDLSGSERQKKTKAEGDRLKEGIYINRGLLCLGNVISALGDD

Parental  KKGGFVPYRDSKLTRLLQDSLGGNSHTLMIACVSPADSNLEETLNTLRYADRARKIKNKPIVNIDPQTAE
          KKGGFVPYRDSKLTRLLQDSLGGNSHTLMIACVSPADSNLEETLNTLRYADRARKIKNKPIVNIDPQTAE
Retrocopy KKGGFVPYRDSKLTRLLQDSLGGNSHTLMIACVSPADSNLEETLNTLRYADRARKIKNKPIVNIDPQTAE

Parental  LNHLKQQVQQLQVLLLQAHGGTLPGSINMEPSENLQSLMEKNQSLVEENEKLSRGLSEAAGQTAQMLERI
          LNHLKQQVQQLQVLLLQA.G.TLPGSINMEPSENL..............EKLSRGLSEAAGQTAQMLERI
Retrocopy LNHLKQQVQQLQVLLLQARGSTLPGSINMEPSENLXXXXXXXXXXXXXXEKLSRGLSEAAGQTAQMLERI

Parental  ILTEQANEKMNAKLEELRQHAACKLNLQKLVETLEDEELKENVEIICNLQQLITQLSDETVACMAAAIDT
          ILTEQANEKM.AKLEELR.HAACKLNLQKLVETLEDEELKENVEIICNLQQLITQLSDETVACM.AAIDT
Retrocopy ILTEQANEKMSAKLEELRHHAACKLNLQKLVETLEDEELKENVEIICNLQQLITQLSDETVACMVAAIDT

Parental  AVEQEAQVETSPEMSRSSDTFTTQHALRQAQMSKELIELNKALALKEALAKKMTQNDSQLQPIQFQYQDN
          .VEQEAQVETSPEMSRSSD.FTTQHALRQAQMSKELIELNKALALKEALA.KMTQNDSQLQPIQFQYQDN
Retrocopy VVEQEAQVETSPEMSRSSDGFTTQHALRQAQMSKELIELNKALALKEALARKMTQNDSQLQPIQFQYQDN

Parental  IKGLELEVISLQKEKEELVLELQTAKKDFNQAKLSERRRKRLQELEGQIADLKKKLNEQSKLLKLKESTE
          IKGLELEVI.LQKEKEELVLE.QTAKKD.NQAKLSE.RRKRLQELEGQIADLKKKLNEQSKLLKLKESTE
Retrocopy IKGLELEVINLQKEKEELVLEVQTAKKDVNQAKLSEHRRKRLQELEGQIADLKKKLNEQSKLLKLKESTE

Parental  HTVSKLNQEIRMMKNQRVQLMRQMKEDAEKFRQWKQKKDKEVIQLKERDRKRQYELLKLERNFQKQSNVL
          HTV.KLNQEIRMMKNQRVQLMRQMKEDAEKFRQWKQKKDKEVIQLKERDRKRQYELLKLERN.QKQSNVL
Retrocopy HTVTKLNQEIRMMKNQRVQLMRQMKEDAEKFRQWKQKKDKEVIQLKERDRKRQYELLKLERNLQKQSNVL

Parental  RRKTEEAAAANKRLKDALQKQQEVADKRKETQSRGMESTAARVKNWLGNEIEVMVSTEEAKRHLNDLLED
          RRKTEEAAAANKRLKDALQKQQEV.DKRKETQSRGMESTAARVK.WLGNEIEVMVSTEEA.RHLNDLLED
Retrocopy RRKTEEAAAANKRLKDALQKQQEVVDKRKETQSRGMESTAARVKTWLGNEIEVMVSTEEARRHLNDLLED

Parental  RKILAQDVAQLKEKKESGENPPPKLRRRTFSLTEVRGQVSESEDSITKQIESLETEMEFRSAQIADLQQK
          RKILAQDVAQLK.KKESGENPPPKLRR.TFSLTE...QVSESEDSITKQIESLETEMEFR.AQIADLQQK
Retrocopy RKILAQDVAQLKKKKESGENPPPKLRRCTFSLTEGHAQVSESEDSITKQIESLETEMEFRNAQIADLQQK

Parental  LLDAESEDRPKQRWENIATIVEAKCALKYLIGELVSSKIQVSKLESSLKQSKASCADTQKMLFEERNHFA
          L.DAESEDRPKQRWENIATIVEAKCALKYLIGELVSSKIQV.KLESSLKQSKASCAD..K.LFEE.NHFA
Retrocopy LIDAESEDRPKQRWENIATIVEAKCALKYLIGELVSSKIQVIKLESSLKQSKASCADMKKTLFEEQNHFA

Parental  EIETELQAELVRMEQQHQEKVLYLLSQLQQSQMAEKQLEESISEKEQQLLSTLKCQDEELEKMREVCEQN
          .IETELQAELVRMEQQHQEKVLYLL.QLQQSQMAEKQLEESISEKEQQ.LSTLKCQD.EL.KMREVCEQN
Retrocopy QIETELQAELVRMEQQHQEKVLYLLGQLQQSQMAEKQLEESISEKEQQQLSTLKCQD-ELDKMREVCEQN

Parental  QQLLRENEIIKQKLTLLQVASRQKPLPKDALLSPDSSFEYIPPKPKPS--KEKFLEQSMDIEDLKYCSEH
          QQLLRENEIIKQKLTLLQV.SRQKPLPKDALLSPDSSFEYIPPKPKPS..KEKFLEQSMDIEDLKYCSEH
Retrocopy QQLLRENEIIKQKLTLLQVSSRQKPLPKDALLSPDSSFEYIPPKPKPSRVKEKFLEQSMDIEDLKYCSEH

Parental  SVNEPEDGDGDGDEGDDKEWKPTKLVKVTRKNIQG
          SVNE.EDGDGD.DEGDD.EWKPTKLVKV.RKN.QG
Retrocopy SVNEHEDGDGDSDEGDDEEWKPTKLVKVSRKNVQG

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	0.09 RPM	6.86 RPM
SRP051959_heart	0.02 RPM	0.32 RPM
SRP051959_kidney	0.02 RPM	0.22 RPM
SRP051959_liver	0.04 RPM	0.28 RPM
SRP051959_lung	0.05 RPM	1.42 RPM
SRP051959_lymph_node	0.09 RPM	2.69 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.11 RPM
SRP051959_spleen	0.06 RPM	2.42 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2142 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2142 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2142 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015566	1 retrocopy	retro_cjac_2142 ,
Cavia porcellus	ENSCPOG00000000211	1 retrocopy	retro_cpor_681,
Homo sapiens	ENSG00000090889	1 retrocopy	retro_hsap_18,
Gorilla gorilla	ENSGGOG00000006631	1 retrocopy	retro_ggor_2218,
Myotis lucifugus	ENSMLUG00000011048	1 retrocopy	retro_mluc_114,
Mus musculus	ENSMUSG00000034311	1 retrocopy	retro_mmus_268,
Pongo abelii	ENSPPYG00000020438	1 retrocopy	retro_pabe_2700,
Rattus norvegicus	ENSRNOG00000038035	1 retrocopy	retro_rnor_2330,