RetrogeneDB ID: retro_cjac_1859

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:158327402..158328374(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021847
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_1859
AACAAGAGACTGAAGTATTATACAGGTAACTATGATCAGTATGTGAAGACGCAACTAGAGCTGGAGGAGAACCAGATGAA
GAGGTTTCACTGGGAGCAAGATCAGATCGCACACATGAAGAACTACATTGCGAGGTTTGGCCATGGCAGTGACAAGTTGG
CTTGGCAGGACCAGAGCAAGGAAAAGACACTACAGAAAATGATGGCATCAGGACTGACAGAGAGGGTCGTGAGTGACAAG
ACACTGTCATTTTACTTTCCACCACGTGGCAAGATCCAGCCACCCGTCATTATGGTGCAAAATGTGAGCTTCGAGTATAC
AAAAGATGGGCCTTGCATCTACAATAATCTAGAATTTGGAATTGACCTTGACACACGAGTGGCTCTGTTAGGGCCCAGTG
GAGCAGGAAATTCAACTCTTCCAAAGCTGCTGACTGGAGAGCTACTACCCACAGACGGCATGATCTGAAAACACTCGCAT
GTCAAGATAGGGCGTTACCATCAGCATTTACAAGAGCAGCTGGACTTAGATCTCTCGCCTTTGGAGTACATGATGAAGTG
TTACCCAGAGATCAAGAAGAAGGAAGAAATGAGGAAGATTGTTGGGCGATACGGTCTCACTGGGAAACAACAGGTGAGCT
CAATCCAGAACTTGTCAGATGGGCAGAAATGCCGAGTGTGTCTGGCCTGGCTGGCCTGGCAGAACCCTCACATGCTCTTC
CTGAATGAGGCCACCAATCACCTGGATACTGAGATCATCGACGCCCTGGAAGATGCCATCAATGAGTTTGAGGGTGATAT
GATGCTGGTCAGCCATGACTTCAGACTCATTCAGCAGGTCGCACAGGAAATTTGGGTCTGTGAGAAGCAGACAATCACCA
AGTGGCCTGGAGACATCCTGGCTTACAAGGAGCACCTCAAATCCAAGCTGGTGGATGAGGAGCCCCAGCTCACCAAGAGG
ACCCACAACGTG

Alignment

ORF - retro_cjac_1859 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.9 %
• Parental protein coverage: 51.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NKKLKYYTGNYDQYVKTRLELEENQMKRFHWEQDQIAHMKNYIARFGHGSAKLARQAQSKEKTLQKMMAS
          NK.LKYYTGNYDQYVKT.LELEENQMKRFHWEQDQIAHMKNYIARFGHGS.KLA.Q.QSKEKTLQKMMAS
Retrocopy NKRLKYYTGNYDQYVKTQLELEENQMKRFHWEQDQIAHMKNYIARFGHGSDKLAWQDQSKEKTLQKMMAS

Parental  GLTERVVSDKTLSFYFPPCGKIPPPVIMVQNVSFKYTKDGPCIYNNLEFGIDLDTRVALVGPNGAGKSTL
          GLTERVVSDKTLSFYFPP.GKI.PPVIMVQNVSF.YTKDGPCIYNNLEFGIDLDTRVAL.GP.GAG.STL
Retrocopy GLTERVVSDKTLSFYFPPRGKIQPPVIMVQNVSFEYTKDGPCIYNNLEFGIDLDTRVALLGPSGAGNSTL

Parental  LKLLTGELLPTDGMIRKHSHVKIGRYHQHLQEQLDLDLSPLEYMMKCYPEIKEKEEMRKIIGRYGLTGKQ
          .KLLTGELLPTDGMI.KHSHVKIGRYHQHLQEQLDLDLSPLEYMMKCYPEIK.KEEMRKI.GRYGLTGKQ
Retrocopy PKLLTGELLPTDGMI*KHSHVKIGRYHQHLQEQLDLDLSPLEYMMKCYPEIKKKEEMRKIVGRYGLTGKQ

Parental  QVSPIRNLSDGQKCRVCLAWLAWQNPHMLFLDEPTNHLDIETIDALADAINEFEGGMMLVSHDFRLIQQV
          QVS.I.NLSDGQKCRVCLAWLAWQNPHMLFL.E.TNHLD.E.IDAL.DAINEFEG.MMLVSHDFRLIQQV
Retrocopy QVSSIQNLSDGQKCRVCLAWLAWQNPHMLFLNEATNHLDTEIIDALEDAINEFEGDMMLVSHDFRLIQQV

Parental  AQEIWVCEKQTITKWPGDILAYKEHLKSKLVDEEPQLTKRTHNV
          AQEIWVCEKQTITKWPGDILAYKEHLKSKLVDEEPQLTKRTHNV
Retrocopy AQEIWVCEKQTITKWPGDILAYKEHLKSKLVDEEPQLTKRTHNV

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	13.71 RPM
SRP051959_heart	0.02 RPM	13.80 RPM
SRP051959_kidney	0.02 RPM	12.71 RPM
SRP051959_liver	0.04 RPM	11.24 RPM
SRP051959_lung	0.00 RPM	11.81 RPM
SRP051959_lymph_node	0.00 RPM	11.99 RPM
SRP051959_skeletal_muscle	0.00 RPM	45.90 RPM
SRP051959_spleen	0.02 RPM	11.49 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1859 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1859 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1859 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,