RetrogeneDB ID: retro_cjac_3231

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:80113821..80114334(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000005391
• Aliases: None
• Description: None

Sequence

>retro_cjac_3231
GACAAAGCAGTACAGGTGACCAAGAAAAAAAAAAGAAGAAAGAAGACAATATTCCAACAAAGGATGAATCACTATATGAT
CCTGAAAAAAGATAACAGAGATTAGGCCTGGGTTGATGCACAGAGAAGGGGTTACCATGGTTTGGGATGACAGAGGTCAT
GTCAGCGACAGCCTGTTCCAAATAGTGATGCTGTCTTGAATTATCCTGCCTGCATGACCACACTGTGCCTTGATTGCCAA
AGGCATGAATCATACAAAACTCAATATAGAGTGATGTTTGTGATGAATTCTTTTATTAACAAAGAGGAGGTTCTAAGATA
CAAAGCCTCGGAGAACAGGAGGAAAAGGCGGGACCATAAGAAGATAAGGTCTAACCAGGAAGATGCTGCCTAGAAGGCAG
AGACAGCTGTGGGAGAAATCTATCACCCAGTCATGTGCACCGAATGTTCCACTGAAGTGGTAGTCTATGACAAGGATGAA
GTCTTTCATTTTTTCAATGTTTTAGCAAGCCAT

Alignment

ORF - retro_cjac_3231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.13 %
• Parental protein coverage: 59.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DKAVQVT-KKK-KKKQHKIPTNDELLYDPE-KDNRDQAWVDAQRRGYHGLGRQRSHQQQPVPNSDAVLNC
          DKAVQVT.KKK.KKK...IPT.DE.LYDPE.KDNRD.AWVDAQRRGYHGLG.QRS.Q.QPVPNSDAVLN.
Retrocopy DKAVQVTKKKK<KKKEDNIPTKDESLYDPE>KDNRD*AWVDAQRRGYHGLG*QRSCQRQPVPNSDAVLNY

Parental  PACMTTLCLDCQRHESYKTQYRAMFVMNCSINKEEVLRYKASENRKKRRGHKKMRSNQEDAAEKAETDVE
          PACMTTLCLDCQRHESYKTQYR.MFVMN..INKEEVLRYKASENR.KRR.HKK.RSNQEDAA.KAET.V.
Retrocopy PACMTTLCLDCQRHESYKTQYRVMFVMNSFINKEEVLRYKASENRRKRRDHKKIRSNQEDAA*KAETAVG

Parental  EIYYPVMCTECSTEVAVYDKDEVFHFFNVLASH
          EIY.PVMCTECSTEV.VYDKDEVFHFFNVLASH
Retrocopy EIYHPVMCTECSTEVVVYDKDEVFHFFNVLASH

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	0.00 RPM	10.34 RPM
SRP051959_heart	0.00 RPM	9.17 RPM
SRP051959_kidney	0.00 RPM	13.91 RPM
SRP051959_liver	0.00 RPM	14.17 RPM
SRP051959_lung	0.02 RPM	12.64 RPM
SRP051959_lymph_node	0.02 RPM	14.27 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.74 RPM
SRP051959_spleen	0.00 RPM	13.89 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3231 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3231 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3231 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005391	1 retrocopy	retro_cjac_3231 ,
Cavia porcellus	ENSCPOG00000003005	1 retrocopy	retro_cpor_898,
Myotis lucifugus	ENSMLUG00000013814	1 retrocopy	retro_mluc_596,
Monodelphis domestica	ENSMODG00000014525	1 retrocopy	retro_mdom_1226,
Mustela putorius furo	ENSMPUG00000001029	1 retrocopy	retro_mputfur_19,
Oryctolagus cuniculus	ENSOCUG00000003226	1 retrocopy	retro_ocun_1701,
Ictidomys tridecemlineatus	ENSSTOG00000005273	2 retrocopies	retro_itri_1598, retro_itri_237,
Tupaia belangeri	ENSTBEG00000001306	1 retrocopy	retro_tbel_4258,