RetrogeneDB ID: retro_cjac_3021

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:126296856..126298732(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NEDD4L
• Ensembl ID: ENSCJAG00000003597
• Aliases: None
• Description: None

Sequence

>retro_cjac_3021
CAAAGAGAACCCTCCTCAAGACTGAGGTCATGCAGTGTCACCAACACTGTTGCAGAACAGGCCCATCTACCACCGCCATC
AGTGGCCTATGTACATACCACGCCAGGTCTGCCTTCAGGCTGGCAAGAAAGAAAAGATGCTAAGGGGCGCACATACTATG
TCAAGCATAACAATCAAACCACAACTTGGACTCGACCTATCATGCAGCTTGCCGAAGATGATGCATCCAGATCAGCCACA
AACAGTAACAACCATCTAATCAAGCCTCAGCTCACTGGCCTCATAGCCTCAGCTTGCCAATAGTAAATTTATCTGCCCCG
CTGGAGGGTGCCAAGGACTCACCCTTACGTCGGGCTGTGAAAGACACCCGTTCCAACCCACAGTCCCCACAGCCATCACC
TTACAGCTCCCCCAAACCACAACACAAAGTCACACAGACCTTCTTGCCACCCGGCTGGGAAATTGGATAGCGCCAAACAG
CTGGCCCTTCTTCATTGATCATAACACAAAGACTACAACCTGGGAAGATCCAGAAGACCCGCATTTGAAATTTCTGGTAT
ATATGCGGTCAAAGACATCTTTAAACCCCAACGACCTTGACCCCCTTCCTCCTGGCTGGGAAGAAAGAATTCACTTGGAT
GGCTGAACATTTTATATTGATCATAATAGCAAAATTACTCAGTGAGAAGACCCGAGACTACAGAACCCAGCTATTACTGG
TCTGGCTGTTCCTTACTCCAGAGAATTTAAGCAGAAATATGACTACTTCAGGAAGAAATTAAAGAAACCTGCTGATATTC
CCAATAGGTTTGAAATGAAACTTCACAGAAACAACATATTTGCAGAGTCCTATCAGAGAATTATGTCGGTGAAAATACCA
GATGTCCTAAAAGCTAGACTATGGATTGAGTTTGAATCAGAGAAAGGTCTTGACTATGGGGGTGTGGCTAGAGAATGGTT
CTTCTTACTGTCTAAAGAGATGTTCAACCCCTACTACGGCCTCCTTGAGTACTCTGCAATGGACAACGACACCCCTCAGA
TCAATCCTAATTCAGGCCTTTTTAATGAAGACCATTTGTCCTCCTTCACTTTCACTGGAAGAGTTGCTGGGCTGGCGGTA
TTTCACGGGAAACTCTTAGATGGTTTCTTCATTAGACCATTTTACAAGGTGATGTTGGGAACGCAGATAACCCTGAATGA
CATGGAATCTGTGAATAATGAATAATTCAACTCTTTGAAATGGACCCTGGAGAATGATCCGACTGAGCTGGACCTCATGT
TCTGTATAGATGAAGAAAACTTTGGACAGACATATCAAGCAGATTTGAAGCCCAATGGGTCAGAAATAATGGTCACAAAT
GAAAACAAAAGGGAATATATCGACTTAGTCATCCAGTGGAGATTTGTGAACAGTGTCCAGAAGCAGATGAACACCTTCTT
GGAGGGATTCACAGAACTGTTTCCTATTGATTTGATTAAAATTTTTGATGAAAATGAGCTGGAGTTGCTGATGTGCTGCC
TCGGTGACGTGAATGACTGAAGACAGCATTCTATGTACAAGAATGGCTACTGCCCGAACCACCCTGTCATTCAGTGGTTC
TGGAAGGCTCCGCTGCTCATGGACGCTGAAAAGTGGATCCAGTTACTGCAGTTTGTCACGGGGATATTGTGAGTACCTAT
GAATGGATTTGCTGAACTTTATGGTTCCAATGGTCCTCAGCTGTTTACAATAGGGCAATGGGGCAGTCCTGAGAAACTGC
CCAGAGCTCACACATGCTTTAATCACCTTGACTTACCTCCATATGAAACCTTTGAAGACTTACGAGAGAAACTTCTCATG
GCCATGGAAAATTCTCAAGGATTTGAAGGGGTAGAT

Alignment

ORF - retro_cjac_3021 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.57 %
• Parental protein coverage: 74.94 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QREPSSRLRSCSVTDAVAEQAHLPPPSVAYVHTTPGLPSGWEERKDAKGRTYYVNHNNRTTTWTRPIMQL
          QREPSSRLRSCSVT..VAEQAHLPPPSVAYVHTTPGLPSGW.ERKDAKGRTYYV.HNN.TTTWTRPIMQL
Retrocopy QREPSSRLRSCSVTNTVAEQAHLPPPSVAYVHTTPGLPSGWQERKDAKGRTYYVKHNNQTTTWTRPIMQL

Parental  AEDGASGSATNSSNHLIEPQIRR-PRSLSSPTVTLSAPLEGAKDSPVRRAVKDTLSNPQSPQPSPYNSPK
          AED.AS.SATNS.NHLI.PQ....P.SLS.P.V.LSAPLEGAKDSP.RRAVKDT.SNPQSPQPSPY.SPK
Retrocopy AEDDASRSATNSNNHLIKPQLTG<PHSLSLPIVNLSAPLEGAKDSPLRRAVKDTRSNPQSPQPSPYSSPK

Parental  PQHKVTQSFLPPGWEMR-IAPNGRPFFIDHNTKTTTW---EDPRLKFPVHMRSKTSLNPNDLGPLPPGWE
          PQHKVTQ.FLPPGWE...IAPN..PFFIDHNTKTTTW...EDP.LKF.V.MRSKTSLNPNDL.PLPPGWE
Retrocopy PQHKVTQTFLPPGWEIG<IAPNSWPFFIDHNTKTTTWEDPEDPHLKFLVYMRSKTSLNPNDLDPLPPGWE

Parental  ERIHLDGRTFYIDHNSKITQWEDPRLQNPAITGPAVPYSREFKQKYDYFRKKLKKPADIPNRFEMKLHRN
          ERIHLDG.TFYIDHNSKITQ.EDPRLQNPAITG.AVPYSREFKQKYDYFRKKLKKPADIPNRFEMKLHRN
Retrocopy ERIHLDG*TFYIDHNSKITQ*EDPRLQNPAITGLAVPYSREFKQKYDYFRKKLKKPADIPNRFEMKLHRN

Parental  NIFEESYRRIMSVKRPDVLKARLWIEFESEKGLDYGGVAREWFFLLSKEMFNPYYGLFEYSATDNYTLQI
          NIF.ESY.RIMSVK.PDVLKARLWIEFESEKGLDYGGVAREWFFLLSKEMFNPYYGL.EYSA.DN.T.QI
Retrocopy NIFAESYQRIMSVKIPDVLKARLWIEFESEKGLDYGGVAREWFFLLSKEMFNPYYGLLEYSAMDNDTPQI

Parental  NPNSGLCNEDHLSYFTFIGRVAGLAVFHGKLLDGFFIRPFYKMMLGKQITLNDMESVDSEYYNSLKWILE
          NPNSGL.NEDHLS.FTF.GRVAGLAVFHGKLLDGFFIRPFYK.MLG.QITLNDMESV..E..NSLKW.LE
Retrocopy NPNSGLFNEDHLSSFTFTGRVAGLAVFHGKLLDGFFIRPFYKVMLGTQITLNDMESVNNE*FNSLKWTLE

Parental  NDPTELDLMFCIDEENFGQTYQVDLKPNGSEIMVTNENKREYIDLVIQWRFVNRVQKQMNAFLEGFTELL
          NDPTELDLMFCIDEENFGQTYQ.DLKPNGSEIMVTNENKREYIDLVIQWRFVN.VQKQMN.FLEGFTEL.
Retrocopy NDPTELDLMFCIDEENFGQTYQADLKPNGSEIMVTNENKREYIDLVIQWRFVNSVQKQMNTFLEGFTELF

Parental  PIDLIKIFDENELELLMCGLGDVDVNDWRQHSIYKNGYCPNHPVIQWFWKAVLLMDAEKRIRLLQFVTGT
          PIDLIKIFDENELELLMC.LG..DVND.RQHS.YKNGYCPNHPVIQWFWKA.LLMDAEK.I.LLQFVTG.
Retrocopy PIDLIKIFDENELELLMCCLG--DVND*RQHSMYKNGYCPNHPVIQWFWKAPLLMDAEKWIQLLQFVTGI

Parental  SRVPMNGFAELYGSNGPQLFTIEQWGSPEKLPRAHTCFNRLDLPPYETFEDLREKLLMAVENAQGFEGVD
          ..VPMNGFAELYGSNGPQLFTI.QWGSPEKLPRAHTCFN.LDLPPYETFEDLREKLLMA.EN.QGFEGVD
Retrocopy L*VPMNGFAELYGSNGPQLFTIGQWGSPEKLPRAHTCFNHLDLPPYETFEDLREKLLMAMENSQGFEGVD

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	0.04 RPM	53.21 RPM
SRP051959_heart	0.07 RPM	29.36 RPM
SRP051959_kidney	0.02 RPM	57.35 RPM
SRP051959_liver	0.00 RPM	7.56 RPM
SRP051959_lung	0.03 RPM	78.75 RPM
SRP051959_lymph_node	0.00 RPM	4.22 RPM
SRP051959_skeletal_muscle	0.00 RPM	13.06 RPM
SRP051959_spleen	0.00 RPM	17.42 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3021 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3021 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3021 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003597	1 retrocopy	retro_cjac_3021 ,
Oryctolagus cuniculus	ENSOCUG00000014471	1 retrocopy	retro_ocun_393,