RetrogeneDB ID: retro_cjac_724

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:96752012..96753629(+)
• Located in intron of: ENSCJAG00000014597

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT4
• Ensembl ID: ENSCJAG00000008703
• Aliases: None
• Description: T-complex protein 1 subunit delta [Source:UniProtKB/TrEMBL;Acc:F6YPL5]

Sequence

>retro_cjac_724
ATGCCTGAGAATGTGGCACCCCGGAGTGGGGCGCCTGCCGGGGCTGCCGGCGGCCGCAGGAAGGGCGCCTATCAGGACCG
CGATAAGCAAGCCCAGATCCGCTTCAGCAACATTTCCGCTGACAAAGCGGTTGCTGATGCTATTAGAACAAGCCTTGGAC
CAAAAGGAATGGATAAAATGATTCAAGATGGAAAAGGTGATGTAACCATTACAAATGATGGTGCTACCATTCTGAAACAA
ATGCAAGTATTACATCCAGCAGCAAGAATGCTGGTGGAGCTGTCTAAGGCTCAAGATATAGAAGCAGGAGATGGTACCAC
ATCAGTAGTCATCATTGCTGGCTCTCTCTTAGATTCTTGTACCAAGCTTCTTCAGAAAGGGATTCATCCAACCATCATTT
CCGAGTCATTCCAGAAGGCCCTGGAAAAGGGAATTGAAATCTTGACTGACATGTCTTGACCTGTGGAACTGAGTGACAGA
GAAGCTTTGTTAAATAGTGCAACCACTTCATTGAACCCAAAGGTTGTTTCTCAGTATTCAAGTCTGCTTTCTCCAATGAG
TGTAAATGCAGTGATGAAAGTGATTGACCCAGGAACAGCCACCAGTGTAGATCTTAGAGATATTAAAATAGTTAAGAAGC
TTGGTGGGACAATTGATGACTGTGAGTTGGTGGAAGGGCTGGTTCTTATCCAAAAAGTGTCAAATTCCGGCATAACCAGA
GTTGAAAAGGCCAAGATTGGACTTATTCAGTTTTGCTTATCTGCTCCCAAAACAGATATGGATAATCAAATAGTGGTTTC
TGACTATGCCCAGATGGACCGAGTGCTTCGAGAAGAGAGAGCCTATATTTTAAATTTAGTGAAGCAAATTAAAAAAACAG
GATGTAATGTCCTTCTTATACAGAAGTCTATTCTAAGAGATGCTCTTAGTGATCTTGCATTACACTTTCTGAACAAAATG
AAGATAATGGTGATTAAGGATATTGAAAGAGAAGACATTGAATTTATTTGTAAGACAATTGGAACCAAACCAGTTGCTCA
TATTGACCAATTTACTGCTGACATGCTGGGTTCTGCCGAGTTAGCTGAGGAGGTCAATTTAAATGGTTCTGGCAAACTGC
TCAAGATTACAGGCTGTGCCAGCCCTGGAAAAACAGTTACAATTGTTGTTCGTGGTTCTAACAAACTGGTGATTGAGGAA
GCTGAGCGCTCCATTCATGATGCCCTTTGTGTTATTCGCTGTTTAGTGAAGAAGAGGGCTCTTATCGCAGGAGGTGGCGC
TCCAGAAATAGAGTTGGCCCTACGATTAACTGAATATTCGCGAACACTGAGTGGTATGGAATCCTACTGTGTTCGTGCTT
TTGCAGATGCTATGGAGGTCATTCCATCTACACTAGCTGAAAATGCCGGCCTGAATCCCATTTCTACAGTTACAGAACTA
AGAAACCGGCATGCCCAGGGAGAAAAAACTGCAGGCATTAATGTCAGAAAGGGTGGTATTTCCAACATTTTGGAGGAACT
GGTTGTCCAGCCTCTGTTGGTGTCAGTCAGTGCTCTGACCCTTGCAACTGAAACTGTTCGGAGCATTCTGAAAATTGATG
ATGTGGTAAACACTCAA

Alignment

ORF - retro_cjac_724 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPENVAPRSGAPAGAAGGRGKGAYQDRDKPAQIRFSNISAAKAVADAIRTSLGPKGMDKMIQDGKGDVTI
          MPENVAPRSGAPAGAAGGR.KGAYQDRDK.AQIRFSNISA.KAVADAIRTSLGPKGMDKMIQDGKGDVTI
Retrocopy MPENVAPRSGAPAGAAGGRRKGAYQDRDKQAQIRFSNISADKAVADAIRTSLGPKGMDKMIQDGKGDVTI

Parental  TNDGATILKQMQVLHPAARMLVELSKAQDIEAGDGTTSVVIIAGSLLDSCTKLLQKGIHPTIISESFQKA
          TNDGATILKQMQVLHPAARMLVELSKAQDIEAGDGTTSVVIIAGSLLDSCTKLLQKGIHPTIISESFQKA
Retrocopy TNDGATILKQMQVLHPAARMLVELSKAQDIEAGDGTTSVVIIAGSLLDSCTKLLQKGIHPTIISESFQKA

Parental  LEKGIEILTDMSRPVELSDRETLLNSATTSLNSKVVSQYSSLLSPMSVNAVMKVIDPGTATSVDLRDIKI
          LEKGIEILTDMS.PVELSDRE.LLNSATTSLN.KVVSQYSSLLSPMSVNAVMKVIDPGTATSVDLRDIKI
Retrocopy LEKGIEILTDMS*PVELSDREALLNSATTSLNPKVVSQYSSLLSPMSVNAVMKVIDPGTATSVDLRDIKI

Parental  VKKLGGTIDDCELVEGLVLTQKVSNSGITRVEKAKIGLIQFCLSAPKTDMDNQIVVSDYAQMDRVLREER
          VKKLGGTIDDCELVEGLVL.QKVSNSGITRVEKAKIGLIQFCLSAPKTDMDNQIVVSDYAQMDRVLREER
Retrocopy VKKLGGTIDDCELVEGLVLIQKVSNSGITRVEKAKIGLIQFCLSAPKTDMDNQIVVSDYAQMDRVLREER

Parental  AYILNLVKQIKKTGCNVLLIQKSILRDALSDLALHFLNKMKIMVIKDIEREDIEFICKTIGTKPVAHIDQ
          AYILNLVKQIKKTGCNVLLIQKSILRDALSDLALHFLNKMKIMVIKDIEREDIEFICKTIGTKPVAHIDQ
Retrocopy AYILNLVKQIKKTGCNVLLIQKSILRDALSDLALHFLNKMKIMVIKDIEREDIEFICKTIGTKPVAHIDQ

Parental  FTADMLGSAELAEEVNLNGSGKLLKITGCASPGKTVTIVVRGSNKLVIEEAERSIHDALCVIRCLVKKRA
          FTADMLGSAELAEEVNLNGSGKLLKITGCASPGKTVTIVVRGSNKLVIEEAERSIHDALCVIRCLVKKRA
Retrocopy FTADMLGSAELAEEVNLNGSGKLLKITGCASPGKTVTIVVRGSNKLVIEEAERSIHDALCVIRCLVKKRA

Parental  LIAGGGAPEIELALRLTEYSRTLSGMESYCVRAFADAMEVIPSTLAENAGLNPISTVTELRNRHAQGEKT
          LIAGGGAPEIELALRLTEYSRTLSGMESYCVRAFADAMEVIPSTLAENAGLNPISTVTELRNRHAQGEKT
Retrocopy LIAGGGAPEIELALRLTEYSRTLSGMESYCVRAFADAMEVIPSTLAENAGLNPISTVTELRNRHAQGEKT

Parental  AGINVRKGGISNILEELVVQPLLVSVSALTLATETVRSILKIDDVVNTR
          AGINVRKGGISNILEELVVQPLLVSVSALTLATETVRSILKIDDVVNT.
Retrocopy AGINVRKGGISNILEELVVQPLLVSVSALTLATETVRSILKIDDVVNTQ

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	0.44 RPM	42.07 RPM
SRP051959_heart	0.47 RPM	37.12 RPM
SRP051959_kidney	0.87 RPM	39.58 RPM
SRP051959_liver	0.22 RPM	52.48 RPM
SRP051959_lung	0.65 RPM	38.65 RPM
SRP051959_lymph_node	0.91 RPM	50.66 RPM
SRP051959_skeletal_muscle	0.17 RPM	43.52 RPM
SRP051959_spleen	0.78 RPM	47.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_724 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_724 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_724 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003083	2 retrocopies	retro_cfam_2093, retro_cfam_590,
Callithrix jacchus	ENSCJAG00000008703	1 retrocopy	retro_cjac_724 ,
Equus caballus	ENSECAG00000016982	1 retrocopy	retro_ecab_148,
Microcebus murinus	ENSMICG00000015263	1 retrocopy	retro_mmur_344,
Macaca mulatta	ENSMMUG00000013973	1 retrocopy	retro_mmul_2500,
Monodelphis domestica	ENSMODG00000002882	1 retrocopy	retro_mdom_1402,
Otolemur garnettii	ENSOGAG00000003974	2 retrocopies	retro_ogar_1041, retro_ogar_1931,
Sorex araneus	ENSSARG00000010539	1 retrocopy	retro_sara_7,