RetrogeneDB ID: retro_cjac_2809

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:47804635..47805894(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000006970
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ISYNA1
• Ensembl ID: ENSCJAG00000014230
• Aliases: None
• Description: None

Sequence

>retro_cjac_2809
GCGCAATACGAGTACCGGACAACCCGCGTCAGCCGCGAGGGCGGCGTCCTCAAGGTGCACCCCACGACCACGTGCTTCAC
CTTCCGGACCGTCTGGCGGGTGCCCCGGCTCGGGGTCATGCTTGTCGGCTGGGGCGGGAACAATGGCTCCACGCTCACCA
CCGCGGTGCTGGCCAACCAACTGCTTCTGTACTGGCCCACGCGCAGCGGCCGCAAGGAGGCCAACTACTATGGCTCGCTG
ACTCAGGCGGGCACCCTGAGCCTGGGCTTGGATGCCGAGGGCCAGGAGGTGTTCGTGCCCTTCAGTGTGCTGCTGCCCAT
GGTGGCACCCAACGACCTCGTGTTTGATGGCTGGGACATCTCGTCACTGAACCTCGCCGAGGCGATGCGGCGCGCGAAGG
TGCTGGATTGGGAGCTGCAGGAGCAACTGTGGCCGCACATGGAAGCCGTACGGCCTCGGCCTTCCATCTGCATCCCCGAG
TTCATCCCGGCCAACCAGAGCACGCGCGCGGACAACCTCATCCCGGGCTCGGGCGCACAGCAGCTGGAGCAGATCCGCAA
GGACATCCGAGACTTCCGGTCTAGCGCGGGGCTGGACAAAGTCACCGTGCTGTGGACGGCCAACACAGAGCGCTTCTGTG
AGGTGGTTCCAGGTCTCAACAACACGGCCGAGAACCTGCTGCGCACCATTAAGCTTGGCCTGGAGGTGTCTCCCTCCACG
CTCTTCGCGGTCGCCAGCATCCTGGAGGGCTGCGCCTTCCTCAATGGGTCCCCGTAGAACACCCTGGTGCCAGAGCTCTT
GAGCTCGCGTGTCAGCGCCGGGTTTTCGTGGGCGGAGATGACTTTAAGTCTGGCCAGACCAAAGTCAAGTCCGTGCTCGT
GGACTTCTTCATCAGCTCTGGCCTCAAGACCATGTCCATCGTGAGTTACAACCACCTGGGCAACAACGATGGGCAGAACC
TGTCGGTGCCGTTGCAGTTCCGCTCTAAGGAGGTGTCCAAGAGCAACGTGGTGGACGACATGGTGCAGAGTAACCTAGTG
CTCTATATCCTCGGCGAGGAGCCCGACCACTGCGTGGTCATCAAGTACGTGCCATACGTGGGCGACAGCAAGCCCGCGCT
GGATAAGTATACATCGGAGCTAATGCTGGGTGGGACCAACACGCTGGTGCTGCACAACACTTGCGAGGACTCCCTGCTGG
CCGCACCCATCATGCTAGACCTGGCGCTGCTGACCGAGCTGTGCCAGCACGTGAGCTTC

Alignment

ORF - retro_cjac_2809 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.11 %
• Parental protein coverage: 76.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AQYEYRTTRVSREGGVLKVHPTTTRFTFRTVRQVPRLGVMLVGWGGNNGSTLTAAVLANRLRLSWPTRSG
          AQYEYRTTRVSREGGVLKVHPTTT.FTFRTV..VPRLGVMLVGWGGNNGSTLT.AVLAN.L.L.WPTRSG
Retrocopy AQYEYRTTRVSREGGVLKVHPTTTCFTFRTVWRVPRLGVMLVGWGGNNGSTLTTAVLANQLLLYWPTRSG

Parental  RKEANYYGSLTQAGTVSLGLDAEGQEVFVPFSALLPMVAPNDLVFDGWDISSMNLAEAMRRAKVLDWELQ
          RKEANYYGSLTQAGT.SLGLDAEGQEVFVPFS.LLPMVAPNDLVFDGWDISS.NLAEAMRRAKVLDWELQ
Retrocopy RKEANYYGSLTQAGTLSLGLDAEGQEVFVPFSVLLPMVAPNDLVFDGWDISSLNLAEAMRRAKVLDWELQ

Parental  EQLWPHMEALRPRPSVYIPEFIAANQSTRADNLIPGSRAQQLEQIRKDIRDFRSSAGLDKVVVLWTANTE
          EQLWPHMEA.RPRPS..IPEFI.ANQSTRADNLIPGS.AQQLEQIRKDIRDFRSSAGLDKV.VLWTANTE
Retrocopy EQLWPHMEAVRPRPSICIPEFIPANQSTRADNLIPGSGAQQLEQIRKDIRDFRSSAGLDKVTVLWTANTE

Parental  RFCEVVPGLNDTAENLLRTIELGLEVSPSTLFAVASILEGCAFLNGSPQNTLVP-GALELACQRRVFVGG
          RFCEVVPGLN.TAENLLRTI.LGLEVSPSTLFAVASILEGCAFLNGSP.NTLVP..ALELACQRRVFVGG
Retrocopy RFCEVVPGLNNTAENLLRTIKLGLEVSPSTLFAVASILEGCAFLNGSP*NTLVP<RALELACQRRVFVGG

Parental  DDFKSGQTKVKSVLVDFLISSGLKTMSIVSYNHLGNNDGQNLSAPLQFRSKEVSKSNVVDDMVQSNPVLY
          DDFKSGQTKVKSVLVDF.ISSGLKTMSIVSYNHLGNNDGQNLS.PLQFRSKEVSKSNVVDDMVQSN.VLY
Retrocopy DDFKSGQTKVKSVLVDFFISSGLKTMSIVSYNHLGNNDGQNLSVPLQFRSKEVSKSNVVDDMVQSNLVLY

Parental  MPGEEPDHCVVIKYVPYVGDSKRALDEYTSELMLGGTNTLVLHNTCEDSLLAAPIMLDLALLTELCQRVS
          ..GEEPDHCVVIKYVPYVGDSK.ALD.YTSELMLGGTNTLVLHNTCEDSLLAAPIMLDLALLTELCQ.VS
Retrocopy ILGEEPDHCVVIKYVPYVGDSKPALDKYTSELMLGGTNTLVLHNTCEDSLLAAPIMLDLALLTELCQHVS

Parental  F
          F
Retrocopy F

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	0.00 RPM	0.55 RPM
SRP051959_heart	0.00 RPM	2.49 RPM
SRP051959_kidney	0.00 RPM	2.64 RPM
SRP051959_liver	0.00 RPM	0.93 RPM
SRP051959_lung	0.11 RPM	7.01 RPM
SRP051959_lymph_node	0.00 RPM	11.21 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.76 RPM
SRP051959_spleen	0.04 RPM	5.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2809 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2809 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2809 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014230	6 retrocopies	retro_cjac_2768, retro_cjac_2803, retro_cjac_2809 , retro_cjac_2831, retro_cjac_3817, retro_cjac_435,
Homo sapiens	ENSG00000105655	1 retrocopy	retro_hsap_2918,
Gorilla gorilla	ENSGGOG00000016939	1 retrocopy	retro_ggor_2019,
Nomascus leucogenys	ENSNLEG00000006026	1 retrocopy	retro_nleu_826,