RetrogeneDB ID: retro_cjac_2235

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:56833855..56834830(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WBP1L
• Ensembl ID: ENSCJAG00000018079
• Aliases: None
• Description: WW domain binding protein 1-like [Source:HGNC Symbol;Acc:23510]

Sequence

>retro_cjac_2235
CAAAGCTACATCTGTGACACAGGACACTGCTGTGGACAGTCTCAGTGCTGCAACTGCTACTATGAACTCTGGTGGTTCTG
GCTGGTGTGGACCATCATCATCATCCTGAGCTGCTGCTGTGTCTGCCACCACTGCCGAGCCAAGCACCACCTTCAGGCCC
AGCAGCGGCAACATGAAATCAACCTGATCTCCTACTGAGAAGCCCACAATTACTCAGCGCTGCCATTTTATTTCAGGTTT
TTGACAAACTATTTACTACCTCCTTATGAAGAAGTGGTGAACCGACCTCCAACTCCTCCCCCACCATACAGTGTCTTCCA
GCTACAGCAGCAGGAGCTGCTGCCTCCACAGTGTGGCGCTGCAGGTGGCAGTCCTTCGGGCAGCACTGATCCCACCAGGG
GATCCCAAGGGGCATAGAGCGGCCCCTTGTCTGGGCCCAGCAGAAACAGCACAAGACCTCCCAGCATCGCTGACCCTGAG
CCCTCTGACCTACTAGTTGACTAAGTAGCCACCAAAGCTCCGGGGACGGAGCCCAGTGGCTTTGTGGCTGGCCTGGGGGA
GCTGAACTCAGGGGCCATCCTGGACAAGGATGCAGAGTGTAGGGAGGAGCTGCTGAAAGATGACAGCTCTGAACCTGGCA
GAGAACCACCCGACAGCAAAGAGAAGACACCTGGGAGACATCGCCGCTTCACAGGTGACTCAGGCATTGAAGTGTGTGTG
TGCAACCGGGGCCACCATGACGATGACCTCAAAGAGTTCAACGTGCTCATCGACGATGCTCTGGATGGGCCCCTGGACTT
CTGCGACAGCTGCCATGTGTGGCCCCCTGGTGATGAGGAAGTTCTCTGCCAGCTTTCTGAGGAGCAGGATCGAGAGCCTG
GGCACCCTCACCTGCCACAGCCGCCCACATACCTGCTTCTTAATACCATCAACGAGCAGGACTCTCCCAACTCCCAGAGC
AGCAGCTCTTGCAGC

Alignment

ORF - retro_cjac_2235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.88 %
• Parental protein coverage: 95.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QSYICDTGHCCGQSQCCNYYYELWWFWLVWTIIIILSCCCVCHHRRAKHRLQAQQRQHEINLIAYREAHN
          QSYICDTGHCCGQSQCCN.YYELWWFWLVWTIIIILSCCCVCHH.RAKH.LQAQQRQHEINLI.Y.EAHN
Retrocopy QSYICDTGHCCGQSQCCNCYYELWWFWLVWTIIIILSCCCVCHHCRAKHHLQAQQRQHEINLISY*EAHN

Parental  YSALPFYFRFLPNYLLPPYEEVVNRPPTPPPPYSAFQLQQQQLLPPQCGPAGGSPPGGTDPTRGSQGAQS
          YSALPFYFRFL.NYLLPPYEEVVNRPPTPPPPYS.FQLQQQ.LLPPQCG.AGGSP.G.TDPTRGSQGA.S
Retrocopy YSALPFYFRFLTNYLLPPYEEVVNRPPTPPPPYSVFQLQQQELLPPQCGAAGGSPSGSTDPTRGSQGA*S

Parental  SPLSGPSRSSTRPPSIADPEPSDLPVDRVATKAPGMEPSGSVAGLGELDPGAFLDKDAECREELLKDDSS
          .PLSGPSR.STRPPSIADPEPSDL.VD.VATKAPG.EPSG.VAGLGEL..GA.LDKDAECREELLKDDSS
Retrocopy GPLSGPSRNSTRPPSIADPEPSDLLVD*VATKAPGTEPSGFVAGLGELNSGAILDKDAECREELLKDDSS

Parental  EPGSAPPDSKEKTPGRHRRFTGDSGIEVCVCNRGHHDDDLKEFNTLIDDALDGPLDFCDSCHVRPPGDEE
          EPG..PPDSKEKTPGRHRRFTGDSGIEVCVCNRGHHDDDLKEFN.LIDDALDGPLDFCDSCHV.PPGDEE
Retrocopy EPGREPPDSKEKTPGRHRRFTGDSGIEVCVCNRGHHDDDLKEFNVLIDDALDGPLDFCDSCHVWPPGDEE

Parental  EGLCQPSEEQAREPGHPHLPRPPACLLLNTINEQDSPNSQSSSSPS
          ..LCQ.SEEQ.REPGHPHLP.PP..LLLNTINEQDSPNSQSSSS.S
Retrocopy V-LCQLSEEQDREPGHPHLPQPPTYLLLNTINEQDSPNSQSSSSCS

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	0.00 RPM	25.78 RPM
SRP051959_heart	0.00 RPM	27.52 RPM
SRP051959_kidney	0.00 RPM	32.81 RPM
SRP051959_liver	0.00 RPM	49.02 RPM
SRP051959_lung	0.00 RPM	34.37 RPM
SRP051959_lymph_node	0.00 RPM	34.88 RPM
SRP051959_skeletal_muscle	0.00 RPM	21.49 RPM
SRP051959_spleen	0.00 RPM	45.04 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2235 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2235 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014336	1 retrocopy	retro_btau_855,
Choloepus hoffmanni	ENSCHOG00000007532	1 retrocopy	retro_chof_1174,
Callithrix jacchus	ENSCJAG00000018079	1 retrocopy	retro_cjac_2235 ,
Homo sapiens	ENSG00000166272	1 retrocopy	retro_hsap_3774,
Macaca mulatta	ENSMMUG00000017596	1 retrocopy	retro_mmul_1640,
Pongo abelii	ENSPPYG00000002610	1 retrocopy	retro_pabe_3084,
Tupaia belangeri	ENSTBEG00000005555	1 retrocopy	retro_tbel_3660,
Tursiops truncatus	ENSTTRG00000012618	2 retrocopies	retro_ttru_138, retro_ttru_437,