RetrogeneDB ID: retro_cjac_1051

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:81732412..81733416(-)
• Located in intron of: ENSCJAG00000015888

Retrocopy information

• Ensembl ID: ENSCJAG00000015917
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTPN11
• Ensembl ID: ENSCJAG00000012464
• Aliases: None
• Description: None

Sequence

>retro_cjac_1051
AGATTATTTCATCCAAATATCCCTGGTATGGAGGCAGAAAAACCTATTGTTGACAAGAGGAGTTGACGGCAGTTTTTTGG
CAAGGCCAAGTAAAAGTAATCCTGGAGACTTCACAATTTCCATTAGAAGAAATGGAGCTGTCACCCACTTAAAGATTCAG
AACACTGGTGATTATTATGACCTGTATGGAGGGGAGAAGTTTGTCACTTTAGCTGAGTTGGCCCAGTATTACATGGAACA
TCATGGGCAGTTAAAAGAGAAGAATGGAGATGTTATTGAGCTTAAATATCCAGTGAACTGTCTAGATCCTATCTCCGAAA
GGTGGTTTTATGGACACTTCTCCATGAAAGAGGCAGAGAAACTATTAACTGAAAAAGGAAAACATGGTAGCTTTCATGTA
AAAGAGAGCCAGAGCCACCCTGAGATTTTGTTCTTTCTGTGTGCACCAGCAATAACAAAGGGGAAAGCAATGACAGCAAG
TCTAAAGTGACCCCATGTCATGATTTGCTGTCAGGAACTGAAATATGACATTGATGGAGGAGAATGGTTTGATTCTTTGA
CAGATCTTGTGGAACATTACAAAAAGAATACCATGGTGGAAACATTGTGTACAGTACTACAACTCAAGCAGCCCCTTAAT
ATGACTCATATAAATGCTGTTGAAATAGAAAGCAGAGTTTGAGAACTAAGCAAATTAGCTGAAACCACAGATAAAGTCAA
ACAAGGCTTTTGGGAAGAATTTGAGACACTACAACAAGTGCAAACTTCTCTGCAGCCGAAAAGAGGTTCAAAGGCAAAAA
AACAAAAACAAAAGTGGATATAAAACACCCTGCCCTTTGATCATAACAGGGTTGTCTTAAATGACGATGTTCCCAGTGAG
CTTATTTCAGATTATATCAATGCAAATATCATAATGCCTGAATTTGAAACCAAGTGCAACAATTCAAACCCCAAAAAAGA
GTTACATTACCATACAAGGCTGCCTGCAAAACATGGTGAATGAC

Alignment

ORF - retro_cjac_1051 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.29 %
• Parental protein coverage: 56.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RWFHPNITGVEAE-NLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFAT
          R.FHPNI.G.EAE.NLLLTRGVDGSFLARPSKSNPGDFT.S.RRNGAVTH.KIQNTGDYYDLYGGEKF.T
Retrocopy RLFHPNIPGMEAE>NLLLTRGVDGSFLARPSKSNPGDFTISIRRNGAVTHLKIQNTGDYYDLYGGEKFVT

Parental  LAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSH
          LAEL.QYYMEHHGQLKEKNGDVIELKYP.NC.DP.SERWF.GH.S.KEAEKLLTEKGKHGSF.V.ESQSH
Retrocopy LAELAQYYMEHHGQLKEKNGDVIELKYPVNCLDPISERWFYGHFSMKEAEKLLTEKGKHGSFHVKESQSH

Parental  PG-DFVLSVRTGDDKGESNDGKSKVT-HVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQ
          P..DFVLSV.T...KGESND.KSKVT.HVMI.CQELKYD..GGE.FDSLTDLVEHYKKN.MVETL.TVLQ
Retrocopy PE<DFVLSVCTSNNKGESNDSKSKVT>HVMICCQELKYDIDGGEWFDSLTDLVEHYKKNTMVETLCTVLQ

Parental  LKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQR-QENKNKNRYK
          LKQPLN.T.INA.EIESRV.ELSKLAETTDKVKQGFWEEFETLQQ....L....K.G...Q.NKNK..YK
Retrocopy LKQPLNMTHINAVEIESRV*ELSKLAETTDKVKQGFWEEFETLQQVQTSL--QPKRGSK>QKNKNKSGYK

Parental  -NILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSK-PKKSYIATQGCLQNTVND
          .N.LPFDH.RVVL.D..P.E..SDYINANIIMPEFETKCNNS..PKKSYI..QGCLQN.VND
Retrocopy <NTLPFDHNRVVLNDDVPSELISDYINANIIMPEFETKCNNSN>PKKSYITIQGCLQNMVND

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	25.91 RPM
SRP051959_heart	0.00 RPM	57.71 RPM
SRP051959_kidney	0.00 RPM	36.72 RPM
SRP051959_liver	2.92 RPM	37.49 RPM
SRP051959_lung	0.00 RPM	35.40 RPM
SRP051959_lymph_node	0.00 RPM	22.31 RPM
SRP051959_skeletal_muscle	0.00 RPM	70.10 RPM
SRP051959_spleen	0.00 RPM	25.19 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1051 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1051 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1051 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000531	1 retrocopy	retro_cjac_4108,
Callithrix jacchus	ENSCJAG00000005102	1 retrocopy	retro_cjac_1577,
Callithrix jacchus	ENSCJAG00000012464	1 retrocopy	retro_cjac_1051 ,
Homo sapiens	ENSG00000179295	5 retrocopies	retro_hsap_2823, retro_hsap_3061, retro_hsap_3302, retro_hsap_3670, retro_hsap_4062,
Gorilla gorilla	ENSGGOG00000010689	1 retrocopy	retro_ggor_1962,
Macaca mulatta	ENSMMUG00000013253	4 retrocopies	retro_mmul_1501, retro_mmul_1792, retro_mmul_1877, retro_mmul_2345,
Monodelphis domestica	ENSMODG00000003120	1 retrocopy	retro_mdom_516,
Nomascus leucogenys	ENSNLEG00000000078	5 retrocopies	retro_nleu_1200, retro_nleu_1360, retro_nleu_1654, retro_nleu_522, retro_nleu_561,
Pongo abelii	ENSPPYG00000004976	4 retrocopies	retro_pabe_2205, retro_pabe_2535, retro_pabe_2825, retro_pabe_3336,