RetrogeneDB ID: retro_cjac_2721

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:47689705..47691015(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000035478
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_2721
CCCAGGGCATGGCCCGGAGGAAACCAGGTGACGGTGGTGCTCGGTGCACAGTGGGGTGACAAAGGCAAAGGGAAGGTGGT
GGATCTGCTGGCGCAGGACGCCAACATCATGTGCCACTGCCAGGGAGGAAATAATCCTGGCCATACAGTTGTTGTGGATT
CTGTGGACTATGATTTTCATCTCTTACCCAGTGGAATAATTAATCCAAGTGTGGCTGCCTTCATTGGAAATGGTGTGGTA
ATTCATCTACCTGGATTGTTTGAAGAAGCAGAGAAAAATGTTCAAAAAGGAAAAGGACTAGAAGGCTGGGGAAAAAAGGC
TGATTATATCTGACAGAGCTCATACTGTATTTGATTTTCATCAAGCAGCTGATGGTATCCAGGAACAACAGAGACGAGCA
CAAGCAGGAAAAAATTTGGGTACAACAAAAACGGGGAATTGGGCCAGTTTATTCTTCCAAAGCTGCTCAGAGTGGACTTA
GGATGTCAGATCTTGTTTCTGACTTTGATGGCTTCTTGGAGAGGTTTAAAGTTTTAGCCAACCAATACAAATCTATATAC
CCCACTTTGGAAATAGACATCAAAGGTGATTTACAAAAACTCAAGGGTTATATGGAAAGGATTAGGCCAATGGTGAGAGA
TGAAGTTTATTTCCTATATGAGGCCCTACAGGGATCACCAAAGAAACTCTTGGTAGAAGGTTCAAATGCAGCACTAATAG
ATATTGATTTTTGAACTTACCCTTTTGTAATCTCTTCAAATTGTACTGTTGGAGGTGTTTGTACTGGTTTGGGTATACCC
CCTCAAAATGTAGGAGAAATTTATGGAGTTGTGAAAGCTTATACTACTAGAGTTTGTATTGGTGCCTTTCCTACAGAGCA
AGACAATGAAATTGGAAAATTATTACACACAAGGGGTAGAGAGTTTGGTGTAACTACTGGAAGGAAATGAAGATGTGGCT
GGTTGGACCTCGTTTTGCTCAAATATGCTTATATAATCAATGGATTTACTGTGTTGGCACTTACCAAGTTGGATATTTCA
CACATGTTTACGGAAATCAAAGTTGGAGTTGCTTGCAAGTTAGATGGTGAAATCATACCTCATATCCCAGCAAACCAAGA
AGTCTTAAATAAAGTTGAAGTTCAGTATAAGACTCTCCCAGGATGGAACACAGACATATCAAATGCAAGGATGTTTAAAG
AACTACCTGTTAATGCACAAAACTATGTTTGATTTATTAAAGATGAGCTTCAAATTCCAGTTAAATGGATTGGTGTTGGT
GAATCCAGAGAGTCTATGATTCAGCTCTTT

Alignment

ORF - retro_cjac_2721 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.14 %
• Parental protein coverage: 97.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PAASPSGSPRVVTVVLGAQWGDEGKGKVVDLLAQDADIVCRCQGGNNAGHTVVVDSVEYDFHLLPSGIIN
          P.A.P.G....VTVVLGAQWGD.GKGKVVDLLAQDA.I.C.CQGGNN.GHTVVVDSV.YDFHLLPSGIIN
Retrocopy PRAWPGGNQ--VTVVLGAQWGDKGKGKVVDLLAQDANIMCHCQGGNNPGHTVVVDSVDYDFHLLPSGIIN

Parental  PNVTAFIGNGVVIHLPGLFEEAEKNVQKGKGLEGW-EKRLIISDRAHIVFDFHQAADGIQEQQRQEQAGK
          P.V.AFIGNGVVIHLPGLFEEAEKNVQKGKGLEGW.EKRLIISDRAH.VFDFHQAADGIQEQQR..QAGK
Retrocopy PSVAAFIGNGVVIHLPGLFEEAEKNVQKGKGLEGW>EKRLIISDRAHTVFDFHQAADGIQEQQRRAQAGK

Parental  NLGTT-KKGIGPVYSSKAARSGLRMCDLVSDFDGFSERFKVLANQYKSIYPTLEIDIEGELQKLKGYMER
          NLGTT.K.GIGPVYSSKAA.SGLRM.DLVSDFDGF.ERFKVLANQYKSIYPTLEIDI.G.LQKLKGYMER
Retrocopy NLGTT>KRGIGPVYSSKAAQSGLRMSDLVSDFDGFLERFKVLANQYKSIYPTLEIDIKGDLQKLKGYMER

Parental  I-PMVRDGVYFLYE-LTGPPKKILFMVQFHTLKLSDKFLGTYPFVTSSNCTVGGVCTGLGMPPQNVGEVY
          I.PMVRD.VYFLYE.L.G.PKK.L..V......L.D....TYPFV.SSNCTVGGVCTGLG.PPQNVGE.Y
Retrocopy IRPMVRDEVYFLYEALQGSPKKLL--VEGSNAALIDIDF*TYPFVISSNCTVGGVCTGLGIPPQNVGEIY

Parental  GVLKAYTTRVGIGAFPTEQENEIGELLQTRGREFGVTTGRKRRCGWLDLVLLKYAHMINGFTAIRLALTK
          GV.KAYTTRV.IGAFPTEQ.NEIG.LL.TRGREFGVTTGRK.RCGWLDLVLLKYA..INGFT...LALTK
Retrocopy GVVKAYTTRVCIGAFPTEQDNEIGKLLHTRGREFGVTTGRK*RCGWLDLVLLKYAYIINGFTV--LALTK

Parental  LDILDMFTEIKVGVAYKLDGEIIPHIPANQEVLNKVEVQYKTLPGWNTDISNARTFKELPVNAQNYVRFI
          LDI..MFTEIKVGVA.KLDGEIIPHIPANQEVLNKVEVQYKTLPGWNTDISNAR.FKELPVNAQNYV.FI
Retrocopy LDISHMFTEIKVGVACKLDGEIIPHIPANQEVLNKVEVQYKTLPGWNTDISNARMFKELPVNAQNYV*FI

Parental  EDELQIPVKWIGVGKSRESMIQLF
          .DELQIPVKWIGVG.SRESMIQLF
Retrocopy KDELQIPVKWIGVGESRESMIQLF

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	18.99 RPM
SRP051959_heart	0.00 RPM	14.58 RPM
SRP051959_kidney	0.02 RPM	24.67 RPM
SRP051959_liver	0.06 RPM	6.28 RPM
SRP051959_lung	0.02 RPM	17.49 RPM
SRP051959_lymph_node	0.07 RPM	27.51 RPM
SRP051959_skeletal_muscle	0.02 RPM	9.67 RPM
SRP051959_spleen	0.00 RPM	16.09 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2721 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2721 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2721 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,