RetrogeneDB ID: retro_cjac_1807

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:67022040..67022772(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAR2A
• Ensembl ID: ENSCJAG00000003255
• Aliases: None
• Description: None

Sequence

>retro_cjac_1807
GCCGACGCCAACGGGGACAGCGAGTAGGAGAAGGACAAGGACTTAGAAGTTCCAGTTCCTAGCACATTTAATAGACGAGT
ATCAGTCTGTGCTGAGACCTATAACCCTAATGAGGAAGAGGAAGAGGAATATACAGATCCAAGGGTGATTCATCCTAAAA
CTGATGAACAGGGATGCAGACTTCAGGAAACTTGCAAAGATATTCTCCCTTTCAAAAATCTTCATTAGGAACAGCTTTCT
CAAGTTCTCGATGCCATGTTTGAAAGGATAGTCAAAGCTGATGAGCATGTCATTGACCAAGGAGATGATGGAGACAACTT
TTATGTCATAGAACGGGGAACTGATAACATTTTAGTAACAAAAAATAATCAAGCCTGCCCTGTTGCTCAATATGACAACC
ATGGCAGTTTTGGAGAACTAGCTCTGATGCACAACACCCCCGGAACTGCTACCATTCCTGCTACCTCGGAAGGCTCCCTT
CGGGGACTGGACCGGGTGACTTTTAGAAGAATCATAGTGAAAAATAATGCAAAGAAGAGGAAGATGTTTGAAGTATTTAT
TGAGTCTGTGCCCCTCCTTAAATCATTGGAGTTGTCAGAATGAATGACGATTGTGGATATAATAGGAGAGAAGATCTATA
AGGATGGAGAACACATAATTACTCAGGGTGAAAAGGCTGATAGCTTTTACATCATAGAGTCTGGTGAAGTGAGCATTTTG
ATTAGAAGCAAA

Alignment

ORF - retro_cjac_1807 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.7 %
• Parental protein coverage: 59.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADANGDSESEEDEDLEVPVPSRFNRRVSVCAETYNPDEEEED--TDPRVIHPKTDEQRCRLQEACKDILL
          ADANGDSE.E.D.DLEVPVPS.FNRRVSVCAETYNP.EEEE...TDPRVIHPKTDEQ.CRLQE.CKDIL.
Retrocopy ADANGDSE*EKDKDLEVPVPSTFNRRVSVCAETYNPNEEEEEEYTDPRVIHPKTDEQGCRLQETCKDILP

Parental  FKNLDQEQLSQVLDAMFERIVKADEHVIDQGDDGDNFYVIERGTYDILVTKNNQTRSVGQYDNRGSFGEL
          FKNL..EQLSQVLDAMFERIVKADEHVIDQGDDGDNFYVIERGT..ILVTKNNQ...V.QYDN.GSFGEL
Retrocopy FKNLH*EQLSQVLDAMFERIVKADEHVIDQGDDGDNFYVIERGTDNILVTKNNQACPVAQYDNHGSFGEL

Parental  ALMYNTPRAATIVATSEGSLWGLDRVTFRRIIVKNNAKKRKMFESFIESVPLLKSLELSERMKIVDVIGE
          ALM.NTP..ATI.ATSEGSL.GLDRVTFRRIIVKNNAKKRKMFE.FIESVPLLKSLELSE.M.IVD.IGE
Retrocopy ALMHNTPGTATIPATSEGSLRGLDRVTFRRIIVKNNAKKRKMFEVFIESVPLLKSLELSE*MTIVDIIGE

Parental  KIYKDGERIITQGEKADSFYIIESGEVSILIRSK
          KIYKDGE.IITQGEKADSFYIIESGEVSILIRSK
Retrocopy KIYKDGEHIITQGEKADSFYIIESGEVSILIRSK

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	0.22 RPM	28.18 RPM
SRP051959_heart	0.04 RPM	32.52 RPM
SRP051959_kidney	0.18 RPM	21.85 RPM
SRP051959_liver	0.22 RPM	18.19 RPM
SRP051959_lung	0.10 RPM	21.54 RPM
SRP051959_lymph_node	0.14 RPM	18.68 RPM
SRP051959_skeletal_muscle	0.02 RPM	32.60 RPM
SRP051959_spleen	0.02 RPM	27.54 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1807 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1807 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1807 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003255	1 retrocopy	retro_cjac_1807 ,
Monodelphis domestica	ENSMODG00000013392	1 retrocopy	retro_mdom_97,
Oryctolagus cuniculus	ENSOCUG00000012426	1 retrocopy	retro_ocun_538,
Otolemur garnettii	ENSOGAG00000006822	1 retrocopy	retro_ogar_2423,