RetrogeneDB ID: retro_cjac_2193

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:148181226..148182891(+)
• Located in intron of: ENSCJAG00000019105

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCP1
• Ensembl ID: ENSCJAG00000011792
• Aliases: None
• Description: T-complex protein 1 subunit alpha [Source:UniProtKB/TrEMBL;Acc:F6TE24]

Sequence

>retro_cjac_2193
ATGGAGGGGCCTTTGTCGGTGTTCGGGACCGCAGCACTGGGGAGGCGATCCGATCCCAGAACGTTATGGCTGCAGCTTAG
ATTGCCAATATTGTAAAAAGTTCTCTTGGTCCAGTTGGCTTGGATAAAATGTTGGTGGATGATATTGGTGATGTAACCAT
TACTAACGATGGTGCGACAATCCTGAAGTTACTGGAGGTAGAACATCCTGCAGCTAACGTTCTTTGTGAGCTGGCTGATC
TGCAAGACAAAGAAGTTGGAGATGGAACTACCTCAGTGGTTATTATTGCAGCAGAACTCCTAAAAAATGCAGATGAATTA
GTCAAACAGAAAATTCATCCCACATCAGTTATTAGTGGCTATCGACTTGCCTGCAAGGAAGCAGTGCGTTATATTAATGA
AAACCGAATTGTTAACACAGATGAACTAGGAAGAGATTGCCTGATCAATGCTGCTAAGACATCCATGTCTTCCAAAATCA
TTGGAATAAATGGTGATTTCTTTGCTAACATGGTAGTAGATGCTGTACTTGCTATTAAATACACAAATATAAGAGGCCAG
CCGCGCTATCCAGTCAATTCTGTTAATATTTTGAAAGCCCATGGGAGAAGTCAAACGGAGAGTATGCTGATCAGTGGCTA
TGCACTCAACTGTGTGGTAGGATCCCAAGGCATGCCCAAGAGAATTGTAAATACAAAAATTGCTTGCCTTGACTTTAGCC
TGCAAAAAACAAAAATGAAGCTTGGTGTACAGTTGGTCATTACAGACCCTGAAAAACTGGACCAAATTAGACAGAGAGAA
TCAGATATCACCAAGGAGAGAATTCAGAAGATCCTGGCAACTGGTGCCAACATTATTCTAACCACTGGTGGAATTGATGA
TATGTATCTGAAGTATTTTGTGGAGGCTGGTGCTATGGCAGTTAGAAGAGTTTTTAAAAGGGACCTTAAACGCATTGCTA
AAGCTTCTGGAGCATCTATTCTGTCAACCCTGGTGAATTTGGAAGGTGAAGAAACTTTTGAAGTTGCAATGTTGGGACAG
GCAGAAGTGGTCCAAGAGAGAATTTGTGATGATGAGCTGATCTTAATCAAAAACAGTAAGGCTCGTACATCGGCATCGAT
TATCTTATGTGGGGCAAATGATTTCATGTGTGATGAGATGGAGCGCTCTTTACACGATGCCCTTTGTGTAGTGAAGAGAG
TTTTGGAGTCAAAATCTGTGGTTCCAGGTGGGGGTGCTGTAGAAGCAGCCCTGTCCATATACCTTGAAAACTATGCAACC
AGCATGGGGTCTCAGGAACAGCTTGCTATTGCAGAGTTTGCAAGATCACTTCTTGTTATTCCTAATACACTGGCAGTTAA
TGCTGCCCAGAACTCCACAGATCTGGTTGCAAAATTAAGAGCTTTTCACAATGAGGCTCAGGTTAACCTAGAACGTAAAA
AATCTAAAATGGATTGGTCTTGATTTGAGCAATGGTAAACCTCGAGACAACAAACAAGCAGGGGTGTTTGAACCAACCAT
AGTTAAAGTTAAGAGTTTTAAATTTGCAACAGAAGCTGCAATTACCATTCTTCGAATTGATGATCTTATTAAATTACATC
CAGAAAGTAAAGATGATAAACATGGAAGTTATGAAGATGCTGTTCACTCTGGAGCCCTTAATGAT

Alignment

ORF - retro_cjac_2193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEGPLSVFG-DRSTGEAIRSQNVMAAASIANIVKSSLGPVGLDKMLVDDIGDVTITNDGATILKLLEVEH
          MEGPLSVFG.DRSTGEAIRSQNVMAAA.IANIVKSSLGPVGLDKMLVDDIGDVTITNDGATILKLLEVEH
Retrocopy MEGPLSVFG<DRSTGEAIRSQNVMAAA*IANIVKSSLGPVGLDKMLVDDIGDVTITNDGATILKLLEVEH

Parental  PAAKVLCELADLQDKEVGDGTTSVVIIAAELLKNADELVKQKIHPTSVISGYRLACKEAVRYINENLIVN
          PAA.VLCELADLQDKEVGDGTTSVVIIAAELLKNADELVKQKIHPTSVISGYRLACKEAVRYINEN.IVN
Retrocopy PAANVLCELADLQDKEVGDGTTSVVIIAAELLKNADELVKQKIHPTSVISGYRLACKEAVRYINENRIVN

Parental  TDELGRDCLINAAKTSMSSKIIGINGDFFANMVVDAVLAIKYTDIRGQPRYPVNSVNILKAHGRSQTESM
          TDELGRDCLINAAKTSMSSKIIGINGDFFANMVVDAVLAIKYT.IRGQPRYPVNSVNILKAHGRSQTESM
Retrocopy TDELGRDCLINAAKTSMSSKIIGINGDFFANMVVDAVLAIKYTNIRGQPRYPVNSVNILKAHGRSQTESM

Parental  LISGYALNCVVGSQGMPKRIVNAKIACLDFSLQKTKMKLGVQVVITDPEKLDQIRQRESDITKERIQKIL
          LISGYALNCVVGSQGMPKRIVN.KIACLDFSLQKTKMKLGVQ.VITDPEKLDQIRQRESDITKERIQKIL
Retrocopy LISGYALNCVVGSQGMPKRIVNTKIACLDFSLQKTKMKLGVQLVITDPEKLDQIRQRESDITKERIQKIL

Parental  ATGANVILTTGGIDDMCLKYFVEAGAMAVRRVLKRDLKRIAKASGASILSTLANLEGEETFEAAMLGQAE
          ATGAN.ILTTGGIDDM.LKYFVEAGAMAVRRV.KRDLKRIAKASGASILSTL.NLEGEETFE.AMLGQA.
Retrocopy ATGANIILTTGGIDDMYLKYFVEAGAMAVRRVFKRDLKRIAKASGASILSTLVNLEGEETFEVAMLGQA-

Parental  EVVQERICDDELILIKNTKARTSASIILRGANDFMCDEMERSLHDALCVVKRVLESKSVVPGGGAVEAAL
          EVVQERICDDELILIKN.KARTSASIIL.GANDFMCDEMERSLHDALCVVKRVLESKSVVPGGGAVEAAL
Retrocopy EVVQERICDDELILIKNSKARTSASIILCGANDFMCDEMERSLHDALCVVKRVLESKSVVPGGGAVEAAL

Parental  SIYLENYATSMGSREQLAIAEFARSLLVIPNTLAVNAAQDSTDLVAKLRAFHNEAQVNPER-KNLKWIGL
          SIYLENYATSMGS.EQLAIAEFARSLLVIPNTLAVNAAQ.STDLVAKLRAFHNEAQVN.ER.KNLKWIGL
Retrocopy SIYLENYATSMGSQEQLAIAEFARSLLVIPNTLAVNAAQNSTDLVAKLRAFHNEAQVNLER>KNLKWIGL

Parental  DLSNGKPRDNKQAGVFEPTIVKVKSLKFATEAAITILRIDDLIKLHPESKDDKHGSYEDAVHSGALND
          DLSNGKPRDNKQAGVFEPTIVKVKS.KFATEAAITILRIDDLIKLHPESKDDKHGSYEDAVHSGALND
Retrocopy DLSNGKPRDNKQAGVFEPTIVKVKSFKFATEAAITILRIDDLIKLHPESKDDKHGSYEDAVHSGALND

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	1.35 RPM	70.76 RPM
SRP051959_heart	0.60 RPM	52.67 RPM
SRP051959_kidney	0.51 RPM	56.91 RPM
SRP051959_liver	0.28 RPM	71.55 RPM
SRP051959_lung	1.87 RPM	42.59 RPM
SRP051959_lymph_node	0.89 RPM	46.21 RPM
SRP051959_skeletal_muscle	0.52 RPM	53.24 RPM
SRP051959_spleen	0.57 RPM	46.16 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2193 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2193 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2193 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015405	1 retrocopy	retro_amel_828,
Callithrix jacchus	ENSCJAG00000011792	2 retrocopies	retro_cjac_1867, retro_cjac_2193 ,
Equus caballus	ENSECAG00000017953	1 retrocopy	retro_ecab_798,
Homo sapiens	ENSG00000120438	1 retrocopy	retro_hsap_3722,
Gorilla gorilla	ENSGGOG00000014063	1 retrocopy	retro_ggor_2514,
Microcebus murinus	ENSMICG00000007998	1 retrocopy	retro_mmur_795,
Macaca mulatta	ENSMMUG00000012846	1 retrocopy	retro_mmul_1696,
Oryctolagus cuniculus	ENSOCUG00000013847	1 retrocopy	retro_ocun_1577,
Pongo abelii	ENSPPYG00000017146	1 retrocopy	retro_pabe_3135,
Pan troglodytes	ENSPTRG00000018760	1 retrocopy	retro_ptro_2617,
Pteropus vampyrus	ENSPVAG00000005316	1 retrocopy	retro_pvam_522,
Sorex araneus	ENSSARG00000002463	1 retrocopy	retro_sara_624,
Sarcophilus harrisii	ENSSHAG00000015128	1 retrocopy	retro_shar_830,
Ictidomys tridecemlineatus	ENSSTOG00000005572	1 retrocopy	retro_itri_1274,