RetrogeneDB ID: retro_cjac_1577

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:73979137..73979804(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPN2
• Ensembl ID: ENSCJAG00000005102
• Aliases: None
• Description: Tyrosine-protein phosphatase non-receptor type [Source:UniProtKB/TrEMBL;Acc:F7GM04]

Sequence

>retro_cjac_1577
GAGAAAGAATCAAGTGGTGAAACCAGAACAATATCTCACTTTCATTATACTACCTGGCCAGATTTTGTAGTCCCTGAATC
ACCAGCTTCATTTCTCAATTTCTTGTTTAAAGTGAGACAATCTGGCTCCTTGAACCCTGACCACGGGCCTGCGGTGATCC
ACTGTAGTGCAGGCATTGGGCGCTCTGGCACCTTCTCTCTGGTAGACACTTGTCTTGTTTTGATGGAAAAAGGAGATGAT
ATTAACATTAAACAAGTGTAATTGAACATGAGAAAATACTGAATGGGTCTTATTCAGACCCCAGGTCAACTGAGATTCTC
ATACATGGCTATAATAGCAGGAGCAAAATGTATAAAGGGAGATTCTAGTATACAGAAACAATGGAAAGAACTTTCTAAGG
AAGACTCTTCTCCTGCTTTTGATCATTCACCAAACAAAATAACGACTGAAAAATACAATGGAAACAGAATAGGTCTAGAA
GAAGAAAAACTGACAGGTGACCTATGTACAGGACTTTCCTCTAAAATGCAAGATACAATGGAGGAGAACAGTGAGAGTGC
TCTACGGAGAGGACAGAAAGGCCACCACAGCTCAGAAGGTGCAGCAGATGAAACAGAGTCTAAATGAGGATGAACGAAAA
AGAAAAAGGCCAAGATTGACAGACACC

Alignment

ORF - retro_cjac_1577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.78 %
• Parental protein coverage: 58.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDT
          E...SGETRTISHFHYTTWPDF.VPESPASFLNFLFKVR.SGSLNPDHGPAVIHCSAGIGRSGTFSLVDT
Retrocopy EKESSGETRTISHFHYTTWPDFVVPESPASFLNFLFKVRQSGSLNPDHGPAVIHCSAGIGRSGTFSLVDT

Parental  CLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKCIKGDSSIQKQWKELSKEDLSPAF
          CLVLMEKGDDINIKQV.LNMRKY.MGLIQTP.QLRFSYMAII.GAKCIKGDSSIQKQWKELSKED.SPAF
Retrocopy CLVLMEKGDDINIKQV*LNMRKY*MGLIQTPGQLRFSYMAIIAGAKCIKGDSSIQKQWKELSKEDSSPAF

Parental  DYSPNKITTEKYNGNRIGLEEEKLTGDRCTGLSSKMQDTMEENSESALRKRIR-EDRKATTAQKVQQMKQ
          D.SPNKITTEKYNGNRIGLEEEKLTGD.CTGLSSK....M....E.......R.EDRKATTAQKVQQMKQ
Retrocopy DHSPNKITTEKYNGNRIGLEEEKLTGDLCTGLSSK----MQDTMEENSESALR>EDRKATTAQKVQQMKQ

Parental  RLNENERKRKRPRLTDT
          .LNE.ERKRKRPRLTDT
Retrocopy SLNEDERKRKRPRLTDT

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	15.86 RPM
SRP051959_heart	0.39 RPM	13.23 RPM
SRP051959_kidney	0.07 RPM	18.50 RPM
SRP051959_liver	0.06 RPM	14.06 RPM
SRP051959_lung	0.08 RPM	22.53 RPM
SRP051959_lymph_node	0.11 RPM	34.79 RPM
SRP051959_skeletal_muscle	0.11 RPM	8.84 RPM
SRP051959_spleen	0.19 RPM	28.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1577 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1577 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1577 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000867	1 retrocopy	retro_chof_2231,
Callithrix jacchus	ENSCJAG00000000531	1 retrocopy	retro_cjac_4108,
Callithrix jacchus	ENSCJAG00000005102	1 retrocopy	retro_cjac_1577 ,
Callithrix jacchus	ENSCJAG00000012464	1 retrocopy	retro_cjac_1051,
Dasypus novemcinctus	ENSDNOG00000016588	1 retrocopy	retro_dnov_1466,
Erinaceus europaeus	ENSEEUG00000005636	1 retrocopy	retro_eeur_370,
Echinops telfairi	ENSETEG00000005577	2 retrocopies	retro_etel_1743, retro_etel_1942,
Homo sapiens	ENSG00000175354	2 retrocopies	retro_hsap_1186, retro_hsap_480,
Gorilla gorilla	ENSGGOG00000010259	2 retrocopies	retro_ggor_453, retro_ggor_925,
Loxodonta africana	ENSLAFG00000011818	1 retrocopy	retro_lafr_701,
Macropus eugenii	ENSMEUG00000005156	1 retrocopy	retro_meug_653,
Monodelphis domestica	ENSMODG00000021422	1 retrocopy	retro_mdom_1225,
Nomascus leucogenys	ENSNLEG00000009074	3 retrocopies	retro_nleu_2112, retro_nleu_351, retro_nleu_894,
Otolemur garnettii	ENSOGAG00000028605	1 retrocopy	retro_ogar_3429,
Pongo abelii	ENSPPYG00000008983	3 retrocopies	retro_pabe_1077, retro_pabe_1144, retro_pabe_989,
Pan troglodytes	ENSPTRG00000009884	2 retrocopies	retro_ptro_361, retro_ptro_813,