RetrogeneDB ID: retro_cjac_100

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:157185114..157186803(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000001440
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000011384
• Aliases: None
• Description: None

Sequence

>retro_cjac_100
ATAAGTCCTTGGTCAGACACCCATCCTGTGCCCTCTGGCCAGGTCCTCAGAGACCAGAGCATCTATACCCAGCTGTTGGA
GATGATGCTGCACTTGCGGCAGACCATGAGTGAGCACTTTGTGCAGCTGATGAGCAGGCAGGGCCTGCTGCAGGAACAGA
GGCACACCGAGGCCATCCGTGAGCAGGAAGCCCTCCTAGATCGCTTACTGTGCCAGATGATCAACCTCCTACAGTCTGGG
GCCATGAGCGGCCTGGAGCTCCAAGTGCCTCTTCCTTCTGAGGACTCTAGGGGTGATGTCAGATATGGGCAGGGGACCCA
ACTATCTGGACAGCCTGATCCAGTCTCCCAACTGAGTGATTGTGAAGCTGCCTTTGTCAGTCGTGACCTATCCAACCGTG
GGATTGACATCTCTGCCCTCTATCAGTCGAAATCCCAGGGCTATAATGCCTACCAAAAAGACAAATATCATAAGGATAAG
AATACCTTGGGCTTCATTAACCTTGGCACCAGTGAGAACAAGCTCTGCATTGATCTGATGACTGAAAGATTGCTAGAAAG
TGACATGAACTGCATTGAAGAGGGCTTGCTGCAGTACGCTGATTGGAGAGGGCAGCCATTCCTGCGGGAAGAAGTGGCCC
GGTTCCTGACCTACTACTGCAGGGCTCCTGCCCCACTTGATCCAGAAAATGTGGTTGTTCTAAATGGCTGCTGCTCTGTC
TTCTCTGTCCTGGCCATGGTTCTGTGTGACCCAGGCGAGGCCTTCCTGATCCCCACTCCCTTTTATGGTGGTTTTGCCTT
TAGCTCCCGCCTGTATGCGAAGGTTGAGTTGATTCCTGTCCACCTGGAGAGTACGATCACTGCAATAAACACCTATCCTT
TCCAGCTCACTGTGGACAAGTTAGAGGAAGCCCTGCTTGAAGCCAGGCTTGAGGGGAAAAACATCCGAGGCCTTGTGCTA
ACCAACCCTCAGAATCCTTTGGGTGACATCTACTCCCCAGACTCACTGATGAAATACCTGGAATTTGCCAAGAGGTATGA
TCTACATGTGATCATAGATGAGATTTACATGCTGTCTGTGTTTGATGAATCCATCACATTCCACAGTGTTCTGAGCATGA
AAAGTTTGCCTGATCGCAACAGGACCCATGTGATCTGGGGTACCAGTAAGGATTTTGGCATCTCTGGCTTCCGCTTTGGT
GCTCTGTACACCCACAACAAGGAGGTAGCCTCTGCGGTCAGTGCCTTCAGCTTCCTCCACAGCATCTCTGGCATCGCCCA
GCACAAGCTGTGTCAACTGCTCCAGAACACAGAATGGATCGACAAAGTGTACCTACCCACCTATCGTTTCCGGCTCAGGA
AAGCTCACAAATATGTCACTGCTAAGCTGAAGTCGTTGGAGATCCCCTTTCACAACCGCAGCTCTGGCCTCTATGTCTGG
ATCAACTTGAAGAAGTACCTGGATCCCTGTACATTTGAAGAAGAACAGCTCCTCTACCGCCGCTTCCTGGACCACAAGCT
GTTGTTATCCTGTGGCAAAGCTTACATGTGTAAGGAGCCAGGCTGGTTCCGCCTCGTCTTTGCAGATGAGCTCCCCCGGC
TAAAATTGGGCATGCGTCGGTTCTGTGATGTGCTGGAGGAGCAGAAGCAGGATTTGAGAGTGAAGCAGTTGAAGCCGCCT
GCCTCCCAA

Alignment

ORF - retro_cjac_100 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.23 %
• Parental protein coverage: 98.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDTLPVPSGQTRSQVLRDQSIYTQLLEVMWHLQQTMREHFVQLMSRQGLLQERRHIQAIREQEALLSRLL
          SDT.PVPSG....QVLRDQSIYTQLLE.M.HL.QTM.EHFVQLMSRQGLLQE.RH..AIREQEALL.RLL
Retrocopy SDTHPVPSG----QVLRDQSIYTQLLEMMLHLRQTMSEHFVQLMSRQGLLQEQRHTEAIREQEALLDRLL

Parental  CQMINLLQSGATSGLEPQ-PLSSEDSRGDVRYGQGTQLAGQPDPVPQLSDCEATFVTRDLSNRGTDISAL
          CQMINLLQSGA.SGLE.Q.PL.SEDSRGDVRYGQGTQL.GQPDPV.QLSDCEA.FV.RDLSNRG.DISAL
Retrocopy CQMINLLQSGAMSGLELQVPLPSEDSRGDVRYGQGTQLSGQPDPVSQLSDCEAAFVSRDLSNRGIDISAL

Parental  YWSSFQDYNAYQKDKYHKDKNPLGFINLGTSENKLCIDLMAERLQESDMNCVEEALLQYPDWRGQPFLRE
          Y.S..Q.YNAYQKDKYHKDKN.LGFINLGTSENKLCIDLM.ERL.ESDMNC.EE.LLQY.DWRGQPFLRE
Retrocopy YQSKSQGYNAYQKDKYHKDKNTLGFINLGTSENKLCIDLMTERLLESDMNCIEEGLLQYADWRGQPFLRE

Parental  EVARFLTYYCRAPAPLDPENVVVLNGCCSVFSALAMVLCDPGEAFLVPTPFYGGFAFSSRLYAKVELIPV
          EVARFLTYYCRAPAPLDPENVVVLNGCCSVFS.LAMVLCDPGEAFL.PTPFYGGFAFSSRLYAKVELIPV
Retrocopy EVARFLTYYCRAPAPLDPENVVVLNGCCSVFSVLAMVLCDPGEAFLIPTPFYGGFAFSSRLYAKVELIPV

Parental  HLESKITAINTYPFQLTVDKLEEALFEARLKVRRIRRSCIHSVKNSLGHPASSHSLCLMVEWLVYRHDLH
          HLES.ITAINTYPFQLTVDKLEEAL.EARL....IR........N.LG...S..SL....E....R.DLH
Retrocopy HLESTITAINTYPFQLTVDKLEEALLEARLEGKNIRGLVLTNPQNPLGDIYSPDSLMKYLEF-AKRYDLH

Parental  VIIDEIYMLSVFDESITFHSVLSMKSLPDRNRTHVVWGTSKDFGISGFRFGALYTHNKEVASVVSAFGYL
          VIIDEIYMLSVFDESITFHSVLSMKSLPDRNRTHV.WGTSKDFGISGFRFGALYTHNKEVAS.VSAF..L
Retrocopy VIIDEIYMLSVFDESITFHSVLSMKSLPDRNRTHVIWGTSKDFGISGFRFGALYTHNKEVASAVSAFSFL

Parental  HSISGITQHKLCQLLRNTEWIDKVYLPTNRFRLREAHKYVTAKLKALEIPFHNRSSGLYVWINLKKYLDP
          HSISGI.QHKLCQLL.NTEWIDKVYLPT.RFRLR.AHKYVTAKLK.LEIPFHNRSSGLYVWINLKKYLDP
Retrocopy HSISGIAQHKLCQLLQNTEWIDKVYLPTYRFRLRKAHKYVTAKLKSLEIPFHNRSSGLYVWINLKKYLDP

Parental  CTFEEEQLLYRRFLDHKLLLSCGKAYMCKEPGWFCLIFADELPRLKLAMRRFCDVLEEQKQDLIVKQLE
          CTFEEEQLLYRRFLDHKLLLSCGKAYMCKEPGWF.L.FADELPRLKL.MRRFCDVLEEQKQDL.VKQL.
Retrocopy CTFEEEQLLYRRFLDHKLLLSCGKAYMCKEPGWFRLVFADELPRLKLGMRRFCDVLEEQKQDLRVKQLK

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	0.09 RPM	0.02 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.02 RPM
SRP051959_liver	0.00 RPM	0.04 RPM
SRP051959_lung	0.11 RPM	0.00 RPM
SRP051959_lymph_node	0.05 RPM	0.02 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.04 RPM	0.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_100 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_100 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_100 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011384	1 retrocopy	retro_cjac_100 ,
Dipodomys ordii	ENSDORG00000005058	1 retrocopy	retro_dord_340,
Equus caballus	ENSECAG00000011908	1 retrocopy	retro_ecab_575,
Echinops telfairi	ENSETEG00000009026	2 retrocopies	retro_etel_1006, retro_etel_204,
Homo sapiens	ENSG00000205126	1 retrocopy	retro_hsap_3553,
Myotis lucifugus	ENSMLUG00000005151	1 retrocopy	retro_mluc_1235,
Nomascus leucogenys	ENSNLEG00000017966	1 retrocopy	retro_nleu_2326,
Ochotona princeps	ENSOPRG00000002097	1 retrocopy	retro_opri_526,
Ochotona princeps	ENSOPRG00000006805	7 retrocopies	retro_opri_1064, retro_opri_1151, retro_opri_251, retro_opri_252, retro_opri_398, retro_opri_399, retro_opri_808,
Pongo abelii	ENSPPYG00000003340	1 retrocopy	retro_pabe_2934,
Pan troglodytes	ENSPTRG00000028662	1 retrocopy	retro_ptro_2414,
Tupaia belangeri	ENSTBEG00000016623	1 retrocopy	retro_tbel_3677,
Tursiops truncatus	ENSTTRG00000002727	1 retrocopy	retro_ttru_1321,