RetrogeneDB ID: retro_cjac_839

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:23802404..23803103(+)
• Located in intron of: ENSCJAG00000008579

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAPTM4A
• Ensembl ID: ENSCJAG00000007433
• Aliases: None
• Description: lysosomal protein transmembrane 4 alpha [Source:HGNC Symbol;Acc:6924]

Sequence

>retro_cjac_839
ATGGTGTCCATGACTTTCAAGCGGAGCTGCAGCGACCGGTTCTACAGCACCCGGTGCTGCGGCTGTTGCCATGTCCGCAC
CGGGACCATCATCCTGGGGACCTGGTACATGGTGGTAAACCTATTGATGGCAATTTTGCTGACTGTGGAAGTGACTCATC
CAAACTCCATGCCAGCTGTCAACATTCAGTATGAAGTCATCGGTAATTACTATTCATCTGAGAGAATGGCTGATAATGCC
TGTGTTCTTTTTGCTGTCTCTGTTCTTATGTTTATAATCAGTTCAATGCTGGTTTATGGAGCAATTTCTTATCAAGTGGG
CTGGCTGATTCCATTCTTCTGTTACCAGCTTTTTGACTTCGTCCTCAGTTGCCTGGTTGCTATTAGTTCTCTCACCTATT
TGCCGAGAATCAAAGAATATCTGGATCAGTTGCCTGATTTTCCCTACAAAGATGACCTCCTGGCCTTGGACTCCAGCTGC
CTCCTGTTCATTGTTCTTGTGTTCTTTGCCTTATTCATCATTTTTAAGGCTTATCTAATCAACTGTGTTTGGAACTGCTA
TAAATACATCAACAACCGAAACATGCCAGAGATTGCTGTGTATTCTGCCTTTGAAGCGCCTCCTCAGTATGTTTTGCCAA
CTTATGAAATGGCCGTGAAAATGCCTGAAAAAGAACCACCACCTCCTTACTTACCTGCC

Alignment

ORF - retro_cjac_839 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.28 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVSMTFKRSRSDRFYSTRCCGCCHVRTGTIILGTWYMVVNLLMAILLTVEVTHPNSMPAVNIQYEVIGNY
          MVSMTFKRS.SDRFYSTRCCGCCHVRTGTIILGTWYMVVNLLMAILLTVEVTHPNSMPAVNIQYEVIGNY
Retrocopy MVSMTFKRSCSDRFYSTRCCGCCHVRTGTIILGTWYMVVNLLMAILLTVEVTHPNSMPAVNIQYEVIGNY

Parental  YSSERMADNACVLFAVSVLMFIISSMLVYGAISYQVGWLIPFFCYRLFDFVLSCLVAISSLTYLPRIKEY
          YSSERMADNACVLFAVSVLMFIISSMLVYGAISYQVGWLIPFFCY.LFDFVLSCLVAISSLTYLPRIKEY
Retrocopy YSSERMADNACVLFAVSVLMFIISSMLVYGAISYQVGWLIPFFCYQLFDFVLSCLVAISSLTYLPRIKEY

Parental  LDQLPDFPYKDDLLALDSSCLLFIVLVFFALFIIFKAYLINCVWNCYKYINNRNVPEIAVYPAFEAPPQY
          LDQLPDFPYKDDLLALDSSCLLFIVLVFFALFIIFKAYLINCVWNCYKYINNRN.PEIAVY.AFEAPPQY
Retrocopy LDQLPDFPYKDDLLALDSSCLLFIVLVFFALFIIFKAYLINCVWNCYKYINNRNMPEIAVYSAFEAPPQY

Parental  VLPTYEMAVKMPEKEPPPPYLPA
          VLPTYEMAVKMPEKEPPPPYLPA
Retrocopy VLPTYEMAVKMPEKEPPPPYLPA

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	6.52 RPM	53.43 RPM
SRP051959_heart	7.38 RPM	59.60 RPM
SRP051959_kidney	6.15 RPM	59.73 RPM
SRP051959_liver	6.63 RPM	61.99 RPM
SRP051959_lung	6.64 RPM	65.13 RPM
SRP051959_lymph_node	5.09 RPM	50.27 RPM
SRP051959_skeletal_muscle	4.56 RPM	40.44 RPM
SRP051959_spleen	10.99 RPM	95.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_839 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_839 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_839 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020894	1 retrocopy	retro_btau_575,
Choloepus hoffmanni	ENSCHOG00000011200	2 retrocopies	retro_chof_1916, retro_chof_2320,
Callithrix jacchus	ENSCJAG00000007433	1 retrocopy	retro_cjac_839 ,
Callithrix jacchus	ENSCJAG00000031235	3 retrocopies	retro_cjac_1368, retro_cjac_1664, retro_cjac_3027,
Echinops telfairi	ENSETEG00000002569	1 retrocopy	retro_etel_591,
Mustela putorius furo	ENSMPUG00000013714	1 retrocopy	retro_mputfur_657,
Ochotona princeps	ENSOPRG00000012401	2 retrocopies	retro_opri_356, retro_opri_474,
Pteropus vampyrus	ENSPVAG00000002909	3 retrocopies	retro_pvam_779, retro_pvam_847, retro_pvam_873,