RetrogeneDB ID: retro_cjac_3093

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:105233054..105233728(+)
• Located in intron of: ENSCJAG00000013536

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKR1A1
• Ensembl ID: ENSCJAG00000013633
• Aliases: None
• Description: aldo-keto reductase family 1, member A1 (aldehyde reductase) [Source:HGNC Symbol;Acc:380]

Sequence

>retro_cjac_3093
GACTGGCTGACCGAGTATCTGGACCTGTACCTGAGGCACTGGCCTTATGCCTTTGAGCAGGGAGACAACCCTTTCCCCAA
GAATGCTGATGGGACTATATGCTATGACTCCACCCACTGCAAGGAGCCTTGGAAGGCTCTGAAGGCACTGGTGGCTAAGG
GGCTGGTGCGGGTGCTAGGCCTGTCCAACTTCAACAGTTGGCAGATTGACAATGTACTCAGTGTGACTTCTGTGCCTCCA
GCTGTCTTGCAGGTGGAATGTTACCCATACTTGACTCAGAATGAGCTCATTGCCCACTGCCAAGCATGCGGCCTGGAAGT
AACTGCTTATAGCCCTCTGGGCTCCTCTGATCATGCCTGATGAGATTCTGATGAGCCTGTCCTGCTGGAGGAACCAGTAG
TCCTGGTGTTGATGAAAAAGTATGGCCAATCTCCAGCTCAGATCTTGCTCAAGTGGCAGGTCCAGTGGAAAGTGATCTGC
ATCCCCAAAAGTATCACTCCTTCTTGAATCCTTCAGAATATCAAGGTGTTTGACTTCACCATTAGCCTGGAAGAGATGAA
GCAGCTAAATGCCCTGAACAAAAATTGGCAATATATTGTGCCTATGCTTATGGGGATGGGAAGAGATTCCCCAGGGATGC
AGGGCATCTTCTGTACCCCTTTAATGACCCATAC

Alignment

ORF - retro_cjac_3093 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.65 %
• Parental protein coverage: 69.23 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DLQLEYLDLYLMHWPYAFERGDNPFPKNADGTIRYDSTHYKETWKALEALVAKGLVRALGLSNFNSRQID
          D...EYLDLYL.HWPYAFE.GDNPFPKNADGTI.YDSTH.KE.WKAL.ALVAKGLVR.LGLSNFNS.QID
Retrocopy DWLTEYLDLYLRHWPYAFEQGDNPFPKNADGTICYDSTHCKEPWKALKALVAKGLVRVLGLSNFNSWQID

Parental  DILSVASVRPAVLQVRTASRSPLHKXIAHCQARGLEVTAYSPLGSSDRAWRDPNEPVLLEEPVVLALAEK
          ..LSV.SV.PAVLQV...........IAHCQA.GLEVTAYSPLGSSD.A..D..EPVLLEEPVVL.L..K
Retrocopy NVLSVTSVPPAVLQVECYPYLTQNELIAHCQACGLEVTAYSPLGSSDHA**DSDEPVLLEEPVVLVLMKK

Parental  YGRSPAQILLRWQVQRKVICIPKSITPSRILQNIKVFDFTFSPEEMKQLNALNKNWRYIVPMLM-VDGKR
          YG.SPAQILL.WQVQ.KVICIPKSITPS.ILQNIKVFDFT.S.EEMKQLNALNKNW.YIVPMLM..DGKR
Retrocopy YGQSPAQILLKWQVQWKVICIPKSITPS*ILQNIKVFDFTISLEEMKQLNALNKNWQYIVPMLM<GDGKR

Parental  VPRDAGHPLYPFNDPY
          .PRDAGH.LYPFNDPY
Retrocopy FPRDAGHLLYPFNDPY

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	0.75 RPM	17.04 RPM
SRP051959_heart	0.74 RPM	7.05 RPM
SRP051959_kidney	0.71 RPM	58.46 RPM
SRP051959_liver	0.24 RPM	47.37 RPM
SRP051959_lung	0.98 RPM	8.38 RPM
SRP051959_lymph_node	0.87 RPM	8.68 RPM
SRP051959_skeletal_muscle	0.55 RPM	2.12 RPM
SRP051959_spleen	0.55 RPM	15.15 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3093 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3093 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004549	1 retrocopy	retro_cfam_558,
Callithrix jacchus	ENSCJAG00000012231	14 retrocopies	retro_cjac_1140, retro_cjac_1167, retro_cjac_1718, retro_cjac_1973, retro_cjac_2550, retro_cjac_3102, retro_cjac_3143, retro_cjac_3297, retro_cjac_3692, retro_cjac_3840, retro_cjac_3872, retro_cjac_3910, retro_cjac_476, retro_cjac_621,
Callithrix jacchus	ENSCJAG00000012250	1 retrocopy	retro_cjac_3038,
Callithrix jacchus	ENSCJAG00000012872	1 retrocopy	retro_cjac_1688,
Callithrix jacchus	ENSCJAG00000013633	2 retrocopies	retro_cjac_3093 , retro_cjac_3334,
Echinops telfairi	ENSETEG00000006450	1 retrocopy	retro_etel_1106,
Macropus eugenii	ENSMEUG00000007370	1 retrocopy	retro_meug_1,
Otolemur garnettii	ENSOGAG00000007175	2 retrocopies	retro_ogar_1522, retro_ogar_2582,
Tarsius syrichta	ENSTSYG00000005301	1 retrocopy	retro_tsyr_1409,
Tursiops truncatus	ENSTTRG00000012180	1 retrocopy	retro_ttru_751,