RetrogeneDB ID: retro_cjac_1803

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:63842985..63844100(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022778
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ALDOA
• Ensembl ID: ENSCJAG00000006874
• Aliases: None
• Description: Fructose-bisphosphate aldolase [Source:UniProtKB/TrEMBL;Acc:F6R6I5]

Sequence

>retro_cjac_1803
CTGTACCAGGAACTTGCTACCACCAGCACCATGCCCTGTCAATATCCACGCTGACCCCAGAGCAGAAGTAGGAGCTGTCT
GACATCATTCACCGCATCGTGGCCCCGGGCAAGGGCAACCTGGCTGCAGATGAGTCCACTGAGAGTATTGCCAAGCGGCT
GCAGTCCATTGGCACTGAGAACACCGAGGAGGACCGGCACTTCTACTGTCAGCTGCTGCTGACAGCTGATGACTGGGTGA
ACCCCCACACCGGGGGCGTCATCCTCTTCCACGAGACACTCTACCAGAAGGGGGATGATGGGCGTCCCTTCCCCCAAGTT
ATCAAATCCAAGGGCGGTGTTGTCGGCATCAAGGTAGACAAGGGCGTGGTCCCCCTGGCAGGCACAAATGGTGAGACCAC
CACCCAAGGGCTGGATGGGCTGTCTGAGTGCTGTGCCCAGTACAAGAAGGATGGTGCTGACTTTGCCAAGTGGCGTTGCG
TGCTGAAGATTGGGGAGCACACCCCCTCAGCCCCCGCCATCATGGAAAATGCCAACCTCCTGGCCTGTTACGCCAGCATC
TGTCAGCAGAATGGCATTGTGCCCATCATGGAGCCTGAAATCCTCCCTGATGGGGACCATGACTTGAAGCGCTGTCAGTA
TGTGACTGAGAAGTTGCTGGCTGCTCTCTACAAGGCTCTGAGCAACCACCACATATACCTGGAAGGCACCTTGCTGAAGC
CCAACATGGTTACCCCAGGCCACGCCTGCACTCAGAAGTTTTCTCACGAGGAGACTGCCATGGCAACTGTCACAGCGCTG
TGCCGCACAGTTCCCCCTGCTGTCCCTGGGATCACCTTCCTTTCTGGAGGCCAGAGGAGGAGGCATCCATCAACCTCAAT
GCCATCAACAAGTGCCTCCTGCAAGCCCTGGGCCCTGACCTTCTCCTACAGCCGAGCCCTGCAGGCCTCTGCCCTGAAGG
CCTGGGGTGGGAAGAAGGAAAACAAGAAGGCGGCGCAGGAGGAGTACATCAAGGGCGCCCTGGCCAACAGCCTCTCATGT
CAAGGAAAGTACACCCCAAGCAGTCAGGCTGGGGCTGCCGCCAGCGAGTCCCTCTTCATCTCTAACCGCGCCTAC

Alignment

ORF - retro_cjac_1803 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.19 %
• Parental protein coverage: 89.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LGKELATTSTMPYQYP-ALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFY
          L..ELATTSTMP.QYP..LTPEQK.ELSDI.HRIVAPGKG.LAADEST.SIAKRLQSIGTENTEE.R.FY
Retrocopy LYQELATTSTMPCQYP<TLTPEQK*ELSDIIHRIVAPGKGNLAADESTESIAKRLQSIGTENTEEDRHFY

Parental  RQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLD
          .QLLLTADD.VNP..GGVILFHETLYQK.DDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLD
Retrocopy CQLLLTADDWVNPHTGGVILFHETLYQKGDDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLD

Parental  GLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDL
          GLSE.CAQYKKDGADFAKWRCVLKIGEHTPSA.AIMENAN.LA.YASICQQNGIVPI.EPEILPDGDHDL
Retrocopy GLSECCAQYKKDGADFAKWRCVLKIGEHTPSAPAIMENANLLACYASICQQNGIVPIMEPEILPDGDHDL

Parental  KRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKFSHEEIAMATVTALRRTVPPAVPGIT
          KRCQYVTEK.LAA.YKALS.HHIYLEGTLLKPNMVTPGHACTQKFSHEE.AMATVTAL.RTVPPAVPGIT
Retrocopy KRCQYVTEKLLAALYKALSNHHIYLEGTLLKPNMVTPGHACTQKFSHEETAMATVTALCRTVPPAVPGIT

Parental  FLSGGQ-SEEEASINLNAINKCPLLK-PWALTFSYGRALQASALKAWGGKKENKKAAQEEYIKRALANSL
          FLSGGQ..EE.ASINLNAINKC.LL..PWALTFSY.RALQASALKAWGGKKENKKAAQEEYIK.ALANSL
Retrocopy FLSGGQ<EEE-ASINLNAINKC-LLQ>PWALTFSYSRALQASALKAWGGKKENKKAAQEEYIKGALANSL

Parental  ACQGKYTPSGQAGAAASESLFISNHAY
          .CQGKYTPS.QAGAAASESLFISN.AY
Retrocopy SCQGKYTPSSQAGAAASESLFISNRAY

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	0.04 RPM	136.63 RPM
SRP051959_heart	0.18 RPM	302.17 RPM
SRP051959_kidney	0.11 RPM	201.54 RPM
SRP051959_liver	0.04 RPM	56.27 RPM
SRP051959_lung	0.03 RPM	87.34 RPM
SRP051959_lymph_node	0.02 RPM	65.11 RPM
SRP051959_skeletal_muscle	0.81 RPM	1812.97 RPM
SRP051959_spleen	0.15 RPM	71.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1803 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1803 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1803 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008221	2 retrocopies	retro_cfam_190, retro_cfam_631,
Callithrix jacchus	ENSCJAG00000006874	1 retrocopy	retro_cjac_1803 ,
Cavia porcellus	ENSCPOG00000007434	1 retrocopy	retro_cpor_951,
Echinops telfairi	ENSETEG00000019230	1 retrocopy	retro_etel_20,
Homo sapiens	ENSG00000149925	1 retrocopy	retro_hsap_740,
Gorilla gorilla	ENSGGOG00000013979	1 retrocopy	retro_ggor_621,
Myotis lucifugus	ENSMLUG00000011210	3 retrocopies	retro_mluc_1172, retro_mluc_2634, retro_mluc_808,
Macaca mulatta	ENSMMUG00000000983	1 retrocopy	retro_mmul_2596,
Monodelphis domestica	ENSMODG00000015696	4 retrocopies	retro_mdom_1236, retro_mdom_1356, retro_mdom_528, retro_mdom_96,
Mus musculus	ENSMUSG00000030695	3 retrocopies	retro_mmus_2160, retro_mmus_42, retro_mmus_90,
Nomascus leucogenys	ENSNLEG00000002152	1 retrocopy	retro_nleu_133,
Oryctolagus cuniculus	ENSOCUG00000006329	1 retrocopy	retro_ocun_1550,
Ochotona princeps	ENSOPRG00000009760	1 retrocopy	retro_opri_914,
Pongo abelii	ENSPPYG00000007244	1 retrocopy	retro_pabe_636,
Pan troglodytes	ENSPTRG00000007983	1 retrocopy	retro_ptro_526,
Rattus norvegicus	ENSRNOG00000023647	7 retrocopies	retro_rnor_1343, retro_rnor_1541, retro_rnor_1796, retro_rnor_1807, retro_rnor_226, retro_rnor_2791, retro_rnor_536,