RetrogeneDB ID: retro_cjac_408

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:70718552..70719527(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC30A9
• Ensembl ID: ENSCJAG00000019226
• Aliases: None
• Description: solute carrier family 30 (zinc transporter), member 9 [Source:HGNC Symbol;Acc:1329]

Sequence

>retro_cjac_408
AAACTGCGCTCCAGAACAGCATCAGTGTTTTTTAAGGGACCAGGAAAAGTGGTGATGGTTGCAATTTGCATCAATGGATT
AAACTGCTTCTTTAAATTTCTTGCCTGGATTTATACTGGTTCAGCAAGTATGTTCTCAGAAGCTATACATTCATTATCTG
ATACTTGTAATCAGGGTTTACTAGCATTGGGCATCAGTAAGTCTGTTCAAACACCAGATCCTTCTCATCCGTACCGATTT
TCGAATATGCGCTGTATTTCTTCACTAATTAGTGGTGTTGGTATTTTCATGATGGGTGCAGGACTATCTTGGTACCATGG
AGTCATGGGATTGCTTCATCCTCAACCAATAGAATCCCTTCTATGGGCCTATTGTATTTTAGCAGGATCATTATTATCTG
AAGGAGCGACACTTCTTGTTGCTGTAAATGAACTTCGTAGGAGTGCTCGGACCAAAGGAATGTCGTTTTACCAATATGTA
ATGGAAAGTCGTGATCCTAGTACAAATGTTATATTATTGGAGGATACTGCTGCAGTCTTGGGAGTTATAATAGCAGCCAC
TTGCATGGGTCTTACTTCCGTAACAGGCAATCCACTGTATGACAGCCTAGGTTCTTTGGGTGTGGACACCTTATTAGGCG
TGGTGTCAGCATTCCTCATCTACACTAATACAGAAGCACTCTTAGGGCGGTCCATCCAGCCAGAACAAGCACAGAGGCTC
ACTGAACTCCTGGAGAATGACCCATCAGTAAGGGCAATTCATGATGTTAAAGCCACAGATCTGGGACTAGGTAAAGTAAG
ATTTAAGGCAGAAGTAGATTTTGATGGGCGAGTTGTTACAAAATCATATTTGGAAAAATAAGATTTTGACCAAATGTTAC
AAGAAATTCAAGAAGTGAAAACTCCTGAAGAACTAGAGATCTTTATGCTTAAACATGGAGAAAATATTATTGATACATTA
GGAGCTGAAATAGAC

Alignment

ORF - retro_cjac_408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.92 %
• Parental protein coverage: 59.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KPRSRTASVFFKGPGKVVMVAICINGLNCFFKFLAWIYTGSASMFSEAIHSLSDTCNQGLLALGISKSVQ
          K.RSRTASVFFKGPGKVVMVAICINGLNCFFKFLAWIYTGSASMFSEAIHSLSDTCNQGLLALGISKSVQ
Retrocopy KLRSRTASVFFKGPGKVVMVAICINGLNCFFKFLAWIYTGSASMFSEAIHSLSDTCNQGLLALGISKSVQ

Parental  TPDPSHPYGFSNMRYISSLISGVGIFMMGAGLSWYHGVMGLLHPQPIESLLWAYCILAGSLLSEGATLLV
          TPDPSHPY.FSNMR.ISSLISGVGIFMMGAGLSWYHGVMGLLHPQPIESLLWAYCILAGSLLSEGATLLV
Retrocopy TPDPSHPYRFSNMRCISSLISGVGIFMMGAGLSWYHGVMGLLHPQPIESLLWAYCILAGSLLSEGATLLV

Parental  AVNELRRSARTKGMSFYKYVMESRDPSTNVILLEDTAAVLGVIIAATCMGLTSITGNPLYDSLGSLGVGT
          AVNELRRSARTKGMSFY.YVMESRDPSTNVILLEDTAAVLGVIIAATCMGLTS.TGNPLYDSLGSLGV.T
Retrocopy AVNELRRSARTKGMSFYQYVMESRDPSTNVILLEDTAAVLGVIIAATCMGLTSVTGNPLYDSLGSLGVDT

Parental  LLGVVSAFLIYTNTEALLGRSIQPEQVQRLTELLENDPSVRAIHDVKATDLGLGKVRFKAEVDFDGRVVT
          LLGVVSAFLIYTNTEALLGRSIQPEQ.QRLTELLENDPSVRAIHDVKATDLGLGKVRFKAEVDFDGRVVT
Retrocopy LLGVVSAFLIYTNTEALLGRSIQPEQAQRLTELLENDPSVRAIHDVKATDLGLGKVRFKAEVDFDGRVVT

Parental  RSYLEKQDFDQMLQEIQEVKTPEELEIFMLKHGENIIDTLGAEVD
          .SYLEK.DFDQMLQEIQEVKTPEELEIFMLKHGENIIDTLGAE.D
Retrocopy KSYLEK*DFDQMLQEIQEVKTPEELEIFMLKHGENIIDTLGAEID

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	0.02 RPM	36.45 RPM
SRP051959_heart	0.02 RPM	28.06 RPM
SRP051959_kidney	0.00 RPM	48.28 RPM
SRP051959_liver	0.00 RPM	21.14 RPM
SRP051959_lung	0.07 RPM	30.14 RPM
SRP051959_lymph_node	0.02 RPM	26.64 RPM
SRP051959_skeletal_muscle	0.02 RPM	23.28 RPM
SRP051959_spleen	0.04 RPM	29.10 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_408 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_408 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_408 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019226	1 retrocopy	retro_cjac_408 ,
Cavia porcellus	ENSCPOG00000000374	1 retrocopy	retro_cpor_805,
Otolemur garnettii	ENSOGAG00000000501	1 retrocopy	retro_ogar_3376,
Rattus norvegicus	ENSRNOG00000002246	1 retrocopy	retro_rnor_2805,
Sus scrofa	ENSSSCG00000008801	1 retrocopy	retro_sscr_326,
Ictidomys tridecemlineatus	ENSSTOG00000024271	1 retrocopy	retro_itri_658,