RetrogeneDB ID: retro_cjac_3526

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01183019.1:3778..4828(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABCF2
• Ensembl ID: ENSCJAG00000020371
• Aliases: None
• Description: None

Sequence

>retro_cjac_3526
GAACTAAAAATTTTTAAGCACATCTTGTTCCTCATCCCCCATTTCCAGGATTTTCTGAATGGTGTCTGTACCAACATCCT
TCACAAGAAACTGAAGTATTAAATGGGTAATTATGATCAGTATGTGAAGACGTGGCTAGAGCTGGAGGAGAACCAGATGA
AGTGGTTTCACTGGGAGCAAGATCATATTGCACACATGAAGAACTACATTGCAGGGTTTGGTCATGGTAGTGCCAAGTTG
GCCCAGCAGGCCCAGAGCAAGAAGACACTACAGAAAATGACGGCATCAGGACTCACAGAGAGGGTCATGAGTGACAAGAC
ACTGTCATTTTCTTTCCCACTATGTGGCAAGATCCCTCCACCCATTATTATGGTGCAAAATGTGAGCTTCAAGTATACAA
AAGATGGGCCTTGCATCTACAATAATCTAGAATTTGGAATTGACCTTGACACACAAGTAGCTCTGGTAGGGCCCAATGGA
GTAGGGAAGTCAACTTTTCTGAAGTTGCTAACTGAAGAGCTACTACCCGCAGATGACATGATCCGGAAACACTCTCCTGT
CAAGATAGGGCATTATCATCAGCATTTACAAGAGCAGCTGGACTTAGATCTCTCGCCTTTGGAGTACAAGATGAAATGTT
ACCCAGAGATCAAGGAGAAGGAATAAATGAGGAAGATCATTGGGCAATATGGTCTCACTGGGAAACAACTGGTGAGCCCA
ATCCAGAACTTGTCAGATGGGCAGAAGCACCAAGTGTGTCTGGCCTGGCTGGCCTGGCAGAACCCCCACATGCTCTTCCT
GGATAAGCCCACCAATCACCTTGATATTGAGGCCATCGACACCCTTGCAGATGCCATCAATGAGTTTTAGGGCAGTATGA
TGCTGGTCAGCCATGACTTCAGACTCATTCAGCAGGTTGCACAGGAAATTTGGGTCTGTGAGAAGCAGACAATCACCAAG
TGGCCTGGAGACATCCTGGCTTACAAGGAGCACTTTAAGTCCAAGATGGTGGATGAGGAGCCCCCGCTCACGAAGAGAAC
CCACAACATG

Alignment

ORF - retro_cjac_3526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.72 %
• Parental protein coverage: 56.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELKTFKRILVLVSHSQDFLNGVCTNIIHMHNKKLKYYTGNYDQYVKTRLELEENQMKRFHWEQDQIAHMK
          ELK.FK.IL.L..H.QDFLNGVCTNI.H...KKLKY..GNYDQYVKT.LELEENQMK.FHWEQD.IAHMK
Retrocopy ELKIFKHILFLIPHFQDFLNGVCTNILH---KKLKY*MGNYDQYVKTWLELEENQMKWFHWEQDHIAHMK

Parental  NYIARFGHGSAKLARQAQSKEKTLQKMMASGLTERVVSDKTLSFYFPPCGKIPPPVIMVQNVSFKYTKDG
          NYIA.FGHGSAKLA.QAQSK.KTLQKM.ASGLTERV.SDKTLSF.FP.CGKIPPP.IMVQNVSFKYTKDG
Retrocopy NYIAGFGHGSAKLAQQAQSK-KTLQKMTASGLTERVMSDKTLSFSFPLCGKIPPPIIMVQNVSFKYTKDG

Parental  PCIYNNLEFGIDLDTRVALVGPNGAGKSTLLKLLTGELLPTDGMIRKHSHVKIGRYHQHLQEQLDLDLSP
          PCIYNNLEFGIDLDT.VALVGPNG.GKST.LKLLT.ELLP.D.MIRKHS.VKIG.YHQHLQEQLDLDLSP
Retrocopy PCIYNNLEFGIDLDTQVALVGPNGVGKSTFLKLLTEELLPADDMIRKHSPVKIGHYHQHLQEQLDLDLSP

Parental  LEYMMKCYPEIKEKEEMRKIIGRYGLTGKQQVSPIRNLSDGQKCRVCLAWLAWQNPHMLFLDEPTNHLDI
          LEY.MKCYPEIKEKE.MRKIIG.YGLTGKQ.VSPI.NLSDGQK..VCLAWLAWQNPHMLFLD.PTNHLDI
Retrocopy LEYKMKCYPEIKEKE*MRKIIGQYGLTGKQLVSPIQNLSDGQKHQVCLAWLAWQNPHMLFLDKPTNHLDI

Parental  ETIDALADAINEFEGGMMLVSHDFRLIQQVAQEIWVCEKQTITKWPGDILAYKEHLKSKLVDEEPQLTKR
          E.ID.LADAINEF.G.MMLVSHDFRLIQQVAQEIWVCEKQTITKWPGDILAYKEH.KSK.VDEEP.LTKR
Retrocopy EAIDTLADAINEF*GSMMLVSHDFRLIQQVAQEIWVCEKQTITKWPGDILAYKEHFKSKMVDEEPPLTKR

Parental  THNV
          THN.
Retrocopy THNM

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	2.31 RPM	13.71 RPM
SRP051959_heart	1.40 RPM	13.80 RPM
SRP051959_kidney	0.89 RPM	12.71 RPM
SRP051959_liver	0.87 RPM	11.24 RPM
SRP051959_lung	1.74 RPM	11.81 RPM
SRP051959_lymph_node	2.19 RPM	11.99 RPM
SRP051959_skeletal_muscle	0.76 RPM	45.90 RPM
SRP051959_spleen	2.12 RPM	11.49 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3526 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3526 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3526 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004830	1 retrocopy	retro_cfam_1612,
Callithrix jacchus	ENSCJAG00000020371	3 retrocopies	retro_cjac_1859, retro_cjac_3526 , retro_cjac_381,
Dipodomys ordii	ENSDORG00000012672	1 retrocopy	retro_dord_334,
Echinops telfairi	ENSETEG00000008032	2 retrocopies	retro_etel_1041, retro_etel_1058,
Macaca mulatta	ENSMMUG00000006679	1 retrocopy	retro_mmul_1414,
Oryctolagus cuniculus	ENSOCUG00000000245	1 retrocopy	retro_ocun_765,