RetrogeneDB ID: retro_cjac_452

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:100719720..100720550(+)
• Located in intron of: ENSCJAG00000001769

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADSS
• Ensembl ID: ENSCJAG00000017069
• Aliases: None
• Description: Adenylosuccinate synthetase [Source:UniProtKB/TrEMBL;Acc:F7IRU0]

Sequence

>retro_cjac_452
AAAAATTTGGGTACAACAAAAAAGGGCATTGGGCCGGTTTATTCGTCCAAAGCTGCTCCGAGTGGACTTTGGATGTGCCA
TCTTGTTTCTGACTTCGATGGCTTCTCTGGGAGGTTTAAAGTTCTAGCCAACCAATACAAATCTATATACCTCACTTTGG
AAATAGACATAGAAGGTGAATTACAAACCTCAAGGGTTATATGGAAAGGATTAAACTAATAGTGAGAGAAGGAGTTTATT
TCCTATATGAGGCCCTATATGGATCACCAAAGAAAATCTTGGTAGAAGGTGCAAATGCAGCACTATTAGATATTGATTTG
GAGACTTACCCTTTTGTAAGCTCTTCAAATTGTACTGTTGGAGGTGTTTGTACTGGTTTGGGTATGCCCCCTCAAAATGT
AGGAGAAGTGTATGGAGTTGTGAAAGCTTATACAACTAGAGTTGGTACTGGTGCCTTTCCTACAGAGCACCAAGAAAATG
AAATTGGAGAATTATTACCAACATGGGGTAGAGAGTTTGGTGTAACTACTGGAAGGAAAAGAAGATGTGGCTGGTTGGAC
CTCATTTTGCTCAAATATACTCATATGATCAATGGATTTATTGCATTGGCACTTACCAAGTTGGATATTTTGGACATGTT
TACGGAAATAAAAGTTGGAGTTGCTTACAAGTTAGACAGTGAAATCATACCTCATATCCCAGCAAACCAAGAAGTCTTAA
ATAAAGTTGAAGTTCAGTATAAGACTCTCCCAGGTTGGAACACACGCATATCAAATGCAAGGACATTTAAAGAACTACCT
GTTAATGCACAAAACTATGTTCGATTTATT

Alignment

ORF - retro_cjac_452 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.17 %
• Parental protein coverage: 61.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KNLGTTKKGIGPVYSSKAARSGLRMCDLVSDFDGFSERFKVLANQYKSIYPTLEIDIEGELQ-KLKGYME
          KNLGTTKKGIGPVYSSKAA.SGL.MC.LVSDFDGFS.RFKVLANQYKSIY.TLEIDIEGELQ..LKGYME
Retrocopy KNLGTTKKGIGPVYSSKAAPSGLWMCHLVSDFDGFSGRFKVLANQYKSIYLTLEIDIEGELQ<NLKGYME

Parental  RIPM-VRDGVYFLYE-LTGPPKKILFMVQFHTLKLSDKFLGTYPFVTSSNCTVGGVCTGLGMPPQNVGEV
          RI...VR.GVYFLYE.L.G.PKKIL..V......L.D..L.TYPFV.SSNCTVGGVCTGLGMPPQNVGEV
Retrocopy RIKLIVREGVYFLYEALYGSPKKIL--VEGANAALLDIDLETYPFVSSSNCTVGGVCTGLGMPPQNVGEV

Parental  YGVLKAYTTRVGIGAFPTE-QENEIGELLQTRGREFGVTTGRKRRCGWLDLVLLKYAHMINGFTAIRLAL
          YGV.KAYTTRVG.GAFPTE.QENEIGELL.T.GREFGVTTGRKRRCGWLDL.LLKY.HMINGF.A..LAL
Retrocopy YGVVKAYTTRVGTGAFPTEHQENEIGELLPTWGREFGVTTGRKRRCGWLDLILLKYTHMINGFIA--LAL

Parental  TKLDILDMFTEIKVGVAYKLDGEIIPHIPANQEVLNKVEVQYKTLPGWNTDISNARTFKELPVNAQNYVR
          TKLDILDMFTEIKVGVAYKLD.EIIPHIPANQEVLNKVEVQYKTLPGWNT.ISNARTFKELPVNAQNYVR
Retrocopy TKLDILDMFTEIKVGVAYKLDSEIIPHIPANQEVLNKVEVQYKTLPGWNTRISNARTFKELPVNAQNYVR

Parental  FI
          FI
Retrocopy FI

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	0.78 RPM	18.99 RPM
SRP051959_heart	0.68 RPM	14.58 RPM
SRP051959_kidney	1.35 RPM	24.67 RPM
SRP051959_liver	0.28 RPM	6.28 RPM
SRP051959_lung	0.68 RPM	17.49 RPM
SRP051959_lymph_node	0.25 RPM	27.51 RPM
SRP051959_skeletal_muscle	0.17 RPM	9.67 RPM
SRP051959_spleen	0.34 RPM	16.09 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_452 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_452 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_452 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017069	2 retrocopies	retro_cjac_2721, retro_cjac_452 ,
Homo sapiens	ENSG00000035687	1 retrocopy	retro_hsap_1826,
Monodelphis domestica	ENSMODG00000006559	1 retrocopy	retro_mdom_1431,
Oryctolagus cuniculus	ENSOCUG00000013982	1 retrocopy	retro_ocun_458,
Pongo abelii	ENSPPYG00000000057	1 retrocopy	retro_pabe_1496,
Pan troglodytes	ENSPTRG00000002178	1 retrocopy	retro_ptro_1167,