RetrogeneDB ID: retro_cjac_3334

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:108366084..108367057(-)
• Located in intron of: ENSCJAG00000009402

Retrocopy information

• Ensembl ID: ENSCJAG00000009415
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_3334
ATGGCAGTTTGCTGTGTTCTGCACACTGGGCAAAAGATGTCCCTGATTGGTCTGGGTACCTGGAAGAGTGAACCTGGTCA
GGTAAAAGCAGCGGTTAAGTATGCCCTTAGTGTAGGCTACCACCACATTGACTGTGCTGCTTTCTATGGCAGTGAGCCTG
AGACTGGGGAGGCCCTGAAGGAGGATGTGGGACCAGGCAAGGCAGTGCCTTGGGAGGAGCTGTTTGTGACATCCAAGCTG
TGGAACACCAAGCACCACCCCGAGGATGTTGAGCCTGCCCTCCAGAAGACTCTGGCTGACCTCCAGCTGGGGCATCTGGA
CCTTTACCTGTACGTGATGCACTGGCCTTATGCCTTCGAGCGGGGAGACAATCCCTTCCCCAAGAATGCTGATGGGACTA
TACGCTATGACTCCACCCACTACAAGGAGACTTGGAAGGCTCTGGAGGCACTGGTAGCTAAGGGGCTGGTGCGGGTGCTG
GGCCTGTCCAACTTCAGCAGTCAGCAGATTGATGATATACTCAGTGTGGCCTCCATGCGTCCAGCTGCCTTGCAGGTGGA
ATGTTACCCATACTTGGCTTCGAATGAGCCAATTGCCCACTGCCAAGCATGTGGCCTGGAGGTAACTGCTTATAGCCCTT
TGGGCTCCTCTGATCATGCATGGCGCGATCCTAATGAACTTGTCCTGGAGGAACCAGTAGTCCTGGCGTTGGCTGGAAAG
TATGGCCGATCTGCAGCTCAGATCTTGCTCAGGTGGCAGGTCCAGCAGAAAGTGATCTGCATCCCCAAAAGTATCACTCC
TTCTCGAATCCTTCAGAACATCAAGGTGTTTGACTTCACCTTTGGCTCAGAAGAAATGAAGCAGCTAAATGCCTTGAACA
AAAACTGGCAAGATATTGTGCCTATGCTTATGGTGGATGGGAAGAGTCCTAAGGGATGCAGGGCATCCTCTGTACCCCTT
TAATGACCCATAC

Alignment

ORF - retro_cjac_3334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVSCVLLHTGQKMPLIGLGTWKSEPGQVKAAVKYALSVGYRHIDCAAIYGNEPEIGEALKEDVGPGKAV
          MAV.CVL.HTGQKM.LIGLGTWKSEPGQVKAAVKYALSVGY.HIDCAA.YG.EPE.GEALKEDVGPGKAV
Retrocopy MAVCCVL-HTGQKMSLIGLGTWKSEPGQVKAAVKYALSVGYHHIDCAAFYGSEPETGEALKEDVGPGKAV

Parental  PREELFVTSKLWNTKHHPKDVEPALQKTLADLQLEYLDLYL--MHWPYAFERGDNPFPKNADGTIRYDST
          P.EELFVTSKLWNTKHHP.DVEPALQKTLADLQL..LDLYL..MHWPYAFERGDNPFPKNADGTIRYDST
Retrocopy PWEELFVTSKLWNTKHHPEDVEPALQKTLADLQLGHLDLYLYVMHWPYAFERGDNPFPKNADGTIRYDST

Parental  HYKETWKALEALVAKGLVRALGLSNFNSRQIDDILSVASVRPAVLQVRTASRSPLHKXIAHCQARGLEVT
          HYKETWKALEALVAKGLVR.LGLSNF.S.QIDDILSVAS.RPA.LQV...........IAHCQA.GLEVT
Retrocopy HYKETWKALEALVAKGLVRVLGLSNFSSQQIDDILSVASMRPAALQVECYPYLASNEPIAHCQACGLEVT

Parental  AYSPLGSSDRAWRDPNEPVLLEEPVVLALAEKYGRSPAQILLRWQVQRKVICIPKSITPSRILQNIKVFD
          AYSPLGSSD.AWRDPNE...LEEPVVLALA.KYGRS.AQILLRWQVQ.KVICIPKSITPSRILQNIKVFD
Retrocopy AYSPLGSSDHAWRDPNE-LVLEEPVVLALAGKYGRSAAQILLRWQVQQKVICIPKSITPSRILQNIKVFD

Parental  FTFSPEEMKQLNALNKNWRYIVPMLMVDGKRVPR-DAGHPLYPFNDPY
          FTF..EEMKQLNALNKNW..IVPMLMVDGK..P..DAGHPLYPFNDPY
Retrocopy FTFGSEEMKQLNALNKNWQDIVPMLMVDGKS-PK>DAGHPLYPFNDPY

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	17.04 RPM
SRP051959_heart	0.00 RPM	7.05 RPM
SRP051959_kidney	0.18 RPM	58.46 RPM
SRP051959_liver	0.17 RPM	47.37 RPM
SRP051959_lung	0.11 RPM	8.38 RPM
SRP051959_lymph_node	0.02 RPM	8.68 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.12 RPM
SRP051959_spleen	0.02 RPM	15.15 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3334 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3334 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3334 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,