RetrogeneDB ID: retro_cjac_1512

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:39146040..39147049(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRNT1
• Ensembl ID: ENSCJAG00000015466
• Aliases: None
• Description: None

Sequence

>retro_cjac_1512
GGATGTTGGATGATAAACAACAAAGGAGAAAAGAATAGAATGATTACTGCCAGGCTTCATGAAGAAAATTTTGAGATTAT
GACACTATGTATTGACATCACCACTGATGGAAGATATGCTGAGGCAGGATTTACAACTGACTGAGAGTAAGATGCTGAAT
GCAGAGCTCTCACTATAAATTCTATGTTTTTAGGTTTTGATGGCACGTTATTTGACTACTTTAATGGTTATGAAGATTTA
AAAAATAAGAAACCTAGATTTGTTGGACATGCTAACAGAAAATACAAGAGGATTATCTTAGAAATTTAAGATACTTCAAA
TTTTATGGAAGAATTGTAAACAAACCTGGTGATCATGATACTGAGATTTTGGAAGCAATTGCAGAAAATGCAGAAGACTT
GGCTGGAATATCAGGAGAAAGGATTTGGGTGGAAATAAAAAAATTCTTGTTAGTAACCATGTAAATCCTTTAATTCACCT
TATCTATGATCTTGATGTGACTCCTTATATAGGCTTACCTGCTAATGCAAGTTTAGAAGAATTTGACAAAGTCAGTAAAA
ATGTTGAAGGTTTTTCACCAAAGCCAGTGACACTTTTGGCCTCATTACTCAAAGTACAAGATGATGTCAAAAAATTAGAT
TTGAGGTTGAAGATTGCAAAAGAAGAGAAAAACCTTAGCTTATTTATATTTAAAAAATAGGAAAGACTTAATTAAAGCAC
CAGATAGTTCAGAACCATTGAAACCCTATCGAGACTTCATTATAGATTCTAGGGAACCTGATACGACTACTTGTGTATGT
GAACTACTAAGTACCAAGGAGAGTACTGTGTGCTAATGGAAATACATCAGTGGTACATTCCTCCATTTTCTATAATTGGC
CATGTCATCAGGAAAGTGGAAATTTCTTCAGGAAACGAAATTGGGACTCTATTAGAAGAGTTGGGAGAACAGCAAGAAAA
ATGTGGTTACCAAAAGGAAAAAGACGAATTTCTGAGTTACATAAAGAAG

Alignment

ORF - retro_cjac_1512 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.77 %
• Parental protein coverage: 83.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GIRMINNRGEKHGTITARLHEENFEITTLRIDVTTDGRHAEVEFTTDWQKDAERRDLTINSMFLGFDGTL
          G..MINN.GEK...ITARLHEENFEI.TL.ID.TTDGR.AE..FTTD...DAE.R.LTINSMFLGFDGTL
Retrocopy GCWMINNKGEKNRMITARLHEENFEIMTLCIDITTDGRYAEAGFTTD*E*DAECRALTINSMFLGFDGTL

Parental  FDYFNGYEDLKNKKIRFVGQAK-QRIQEDYLRILRYFRFYGRIVDKPGDHDPETLEAIAENAKGLAGISG
          FDYFNGYEDLKNKK.RFVG.A..Q.IQEDYLR.LRYF.FYGRIV.KPGDHD.E.LEAIAENA..LAGISG
Retrocopy FDYFNGYEDLKNKKPRFVGHAN<QKIQEDYLRNLRYFKFYGRIVNKPGDHDTEILEAIAENAEDLAGISG

Parental  ERIWVELKK-ILVGNHVNHLIHLIYDLDVASYIGLPANASLEEFDKVSKNVEGFSPKPMTLLASLFKVQD
          ERIWVE.KK.ILV.NHVN.LIHLIYDLDV..YIGLPANASLEEFDKVSKNVEGFSPKP.TLLASL.KVQD
Retrocopy ERIWVEIKK<ILVSNHVNPLIHLIYDLDVTPYIGLPANASLEEFDKVSKNVEGFSPKPVTLLASLLKVQD

Parental  DVTKLDLRLKIAKEEKNLGLFI-VKNRKDLIKAADTSEPLKPYQDCIIDSREPDATTRVCELL-KYQGEH
          DV.KLDLRLKIAKEEKNL.LFI..KNRKDLIKA.D.SEPLKPY.D.IIDSREPD.TT.VCELL.KYQGE.
Retrocopy DVKKLDLRLKIAKEEKNLSLFI>LKNRKDLIKAPDSSEPLKPYRDFIIDSREPDTTTCVCELL<KYQGEY

Parental  CLLKEMQQWSIPPFPVSGHDIRKVGISSGKEIGALLQQLREQWKKSGYQMEKDELLSYIKK
          C.L.E..QW.IPPF...GH.IRKV.ISSG.EIG.LL..L.EQ..K.GYQ.EKDE.LSYIKK
Retrocopy CVLMEIHQWYIPPFSIIGHVIRKVEISSGNEIGTLLEELGEQQEKCGYQKEKDEFLSYIKK

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	15.42 RPM
SRP051959_heart	0.00 RPM	21.70 RPM
SRP051959_kidney	0.00 RPM	21.34 RPM
SRP051959_liver	0.00 RPM	15.44 RPM
SRP051959_lung	0.00 RPM	20.66 RPM
SRP051959_lymph_node	0.00 RPM	22.42 RPM
SRP051959_skeletal_muscle	0.00 RPM	17.69 RPM
SRP051959_spleen	0.00 RPM	22.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1512 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1512 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1512 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015466	1 retrocopy	retro_cjac_1512 ,
Dasypus novemcinctus	ENSDNOG00000008837	1 retrocopy	retro_dnov_1635,
Echinops telfairi	ENSETEG00000018177	2 retrocopies	retro_etel_1871, retro_etel_905,
Homo sapiens	ENSG00000072756	2 retrocopies	retro_hsap_246, retro_hsap_2598,
Gorilla gorilla	ENSGGOG00000015286	1 retrocopy	retro_ggor_300,
Nomascus leucogenys	ENSNLEG00000003226	1 retrocopy	retro_nleu_856,
Petromyzon marinus	ENSPMAG00000002236	1 retrocopy	retro_pmar_17,
Pongo abelii	ENSPPYG00000013702	3 retrocopies	retro_pabe_1916, retro_pabe_2721, retro_pabe_412,
Pan troglodytes	ENSPTRG00000014564	1 retrocopy	retro_ptro_1522,