RetrogeneDB ID: retro_cjac_2424

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:31965473..31966667(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000032895
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ERI2
• Ensembl ID: ENSCJAG00000009400
• Aliases: None
• Description: None

Sequence

>retro_cjac_2424
GCAACCAAGCAGCTGGCGCAGCAGCTTGGATTAATTAGGAGAAAGTCAGTTGCATCAGCAAATGGGAACCTAGGAAGAAG
CAAATCCAAGCAGTTGCTTGACTACTTAATTGTCATTGATTTTGAATCGACATGCTGGAATGATGGGAAATGCCACCATA
GCCGGGAAGTAACTGAATTTCCAGCAGTGTTGCTGAACACATCAACTGGACAGATTGAGTCTGAGTTCAGTGCTTATGTT
CAACCTCAGGAACATCCCGTTCTTTCAGAATTTTGCATGGAATTGACAGGCATAAAGCAGGCTCAAGTTGATGAAGGAGT
CCCTCTGAAGATTTGCTTATCTCAGTTCTGTAAATGGATTCATAAGATTCAGCAACAGAAGAAGAACCTTATTTTTGCTG
CTGGGGTTTCAGAGCCTTCTACTTCTGAAGTAAACGCTTATACATTTGTTACGTGGTCAGACTGGGACTTGGGGGTGTGA
CTGGAGTATGAGTGTAAAAGAAAGCAGTTGTTAAAACCAGTGTTTTTAAATTCTTGGATTGATCTCAGAGAAACTTACAA
GCTTTTCTATAGGAGAAAACCAGAAGGACTAAGTGGTGCCTTGCAGGAAGGGGGAATAGAATTCTCAGGACGAGATCATT
CTGGGTTGGACGATTCTCAGAATACTGCCCTTCTTGCTTGGAAAATGGTCAGGGATGGCTGTCTAGTGAAAATTACAAGG
TCGTTGAACAAGGTTCCCACTAAGAAGAATTCCAGCATTCTGGCCAGAAATTTGGATACAAATCAAGTTGAAGAAATGTC
TGCCTGTAACAGCATCCGGGGTCCTAGCATCTATAATAAGGAGCCTAAAAAATACAATAAATTCTATGAAAAAGTTCAAA
TGAAGTCAGTTTGTGCAAATTTTCCTATAAAGGCACAGAAGGATCAATTACAAGTAAAGAACAATATAAAAACAGGTCTT
CACAATGTCAAAAGTTGCTTATCTATTATTAATTCTAAGCCCTCTACTTCTCTGGGGCATTTGCAGTCTCCTACCTTGAA
TTCACCTATCTACATGCAAAAGCAAGGAAAAAATGAACATCTTGCTTTTAATACCAAATCTAAGTCTTCAACAGTTGGTT
CAGAATTGGTGCTTGTTTCTACCAGCATTCTGACTGTTAATCATGTTTCTGATATGGAAATGAGCTCTACTCTT

Alignment

ORF - retro_cjac_2424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.75 %
• Parental protein coverage: 57.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ATKRLARQLGLIRRKSIASANGNLGRSKSKQLFDYLIVIDFESTCWNDGKRHHSQEIIEFPAVLLNTSTG
          ATK.LA.QLGLIRRKS.ASANGNLGRSKSKQL.DYLIVIDFESTCWNDGK.HHS.E..EFPAVLLNTSTG
Retrocopy ATKQLAQQLGLIRRKSVASANGNLGRSKSKQLLDYLIVIDFESTCWNDGKCHHSREVTEFPAVLLNTSTG

Parental  QIESEFHAYVQPQEHPILSEFCMELTGIKQAQVDEGVPLKICLSQFCKWIHKIQQQK-NIIFAAGVSEPS
          QIESEF.AYVQPQEHP.LSEFCMELTGIKQAQVDEGVPLKICLSQFCKWIHKIQQQK.N.IFAAGVSEPS
Retrocopy QIESEFSAYVQPQEHPVLSEFCMELTGIKQAQVDEGVPLKICLSQFCKWIHKIQQQKKNLIFAAGVSEPS

Parental  TSEVNLCAFVTWSDWDLGVCLEYECKRKQLLKPVFLNSWIDLRATYKLFYRRKPKGLSGALQEVGIEFSG
          TSEVN...FVTWSDWDLGV.LEYECKRKQLLKPVFLNSWIDLR.TYKLFYRRKP.GLSGALQE.GIEFSG
Retrocopy TSEVNAYTFVTWSDWDLGV*LEYECKRKQLLKPVFLNSWIDLRETYKLFYRRKPEGLSGALQEGGIEFSG

Parental  REHSGLDDSRNTALLAWKMIKDGCLMKITRSLNKVPTKKNSSILARNLNTNQVEEMSACNSIQGPSIYN-
          R.HSGLDDS.NTALLAWKM..DGCL.KITRSLNKVPTKKNSSILARNL.TNQVEEMSACNSI.GPSIYN.
Retrocopy RDHSGLDDSQNTALLAWKMVRDGCLVKITRSLNKVPTKKNSSILARNLDTNQVEEMSACNSIRGPSIYNK

Parental  EP-KNTINS-HVKVQMKSVCANFPIKAQKDQLQVKNNIKTSLHNVKSCLSIINSKSSTSLGHLQSPTLNS
          EP.KNTINS...KVQMKSVCANFPIKAQKDQLQVKNNIKT.LHNVKSCLSIINSK.STSLGHLQSPTLNS
Retrocopy EP>KNTINS<YEKVQMKSVCANFPIKAQKDQLQVKNNIKTGLHNVKSCLSIINSKPSTSLGHLQSPTLNS

Parental  PIYMQKQGKNEHLAFNTKCESSTVGSELVLVSTTIPTVNHVSDMEMSSTL
          PIYMQKQGKNEHLAFNTK..SSTVGSELVLVST.I.TVNHVSDMEMSSTL
Retrocopy PIYMQKQGKNEHLAFNTKSKSSTVGSELVLVSTSILTVNHVSDMEMSSTL

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	0.11 RPM	4.02 RPM
SRP051959_heart	0.04 RPM	3.03 RPM
SRP051959_kidney	0.07 RPM	6.41 RPM
SRP051959_liver	0.02 RPM	6.11 RPM
SRP051959_lung	0.03 RPM	1.87 RPM
SRP051959_lymph_node	0.00 RPM	1.51 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.01 RPM
SRP051959_spleen	0.08 RPM	2.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2424 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2424 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2424 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003995	1 retrocopy	retro_cjac_3212,
Callithrix jacchus	ENSCJAG00000009400	1 retrocopy	retro_cjac_2424 ,