RetrogeneDB ID: retro_cjac_558

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:81166889..81168215(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022053
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZNF277
• Ensembl ID: ENSCJAG00000016891
• Aliases: None
• Description: None

Sequence

>retro_cjac_558
GTCGCCCGACTGGAGGAAGACCGTGATGGAAGCTGCAGCACAGTCGGGGGTGTAGGTTATGGGGACAGTAAGGATTGTAT
CCTGGAGCCACTTTCCCTGCCAGAAAGTCCAGGTGGCACCACCACTTTAGAAGGTTCTCCATCTGTGCCTTTTATTTTCT
GTGAAGAACATTTTCATGTGGCTGAGCAAGACAAACTTCTGAAGCACATGATTATTGAGCATAAGATTGTCATAGCTGAT
GTCAAATTGGTCGCTGATTTCCAAAGGTACATTTTGTATTGGAGGAAAAGGTTCACTGAACAGCCCATCACAGATTTTTG
TAGTGTGATAAGAATTAATTCCACTGCTCCATTTGAAGAACAAGAGAATTATTTTTTGTTATGTGACGTTTTACCAGAAG
ATAGAATTCTTCGAGAAGAGCTTCAGAAACAGAAACTGAAAGAAATTCTGGAACAACAGCAGCAAGAACGAAATGATAAC
AATTTTCATGGCATTTGTATGTTTTGCAATGAAGAATTCCTTGGAAACAGATCTGTTCTTTTGAACCACATGGCCAGAGA
ACATGCTTTCAACATTGGATTGCCAGACAACATTGTAAACTGCAATGAATTTTTGTGTACATTACAGAAAAAGCTTGACA
ATTTGCAGTGCTTGTACTGTGAGAAGACCTTCAGGGACAAAAATACACTTAAAGATCACATGAGGAAAAAACAGCAACGT
AAGATTAATCCTAAGAACAGAGAATATGATCGATTTTATGTCATCAATTATTTGGAACTTGGAAAATCATGGGAAGAAGT
TCAGTTGGAAGATGATCGGGAGTTGCTGGACAATCAGGAAGATGACTGGTCTGACTGGGAAGAACACCCTGCCTCTGCCG
TCTGCTTATTTTGTGAAAAGCAAGCAGAAACAATTGAGAAATTGTATGTCCACATGGAGGATGCAAACGAATTTAATCTT
CTCAAAATAAAGTCAGAACTTGGATTAAATTTCTATCAGCAAGTGAAACTGGTCAATTTTATTCGGAGGCAAGTTCACCA
GTGCAGATGTTATGGCTGCCATGTGAAGTTCAAATCCAAAGCAGACTTAAGAACTCACATGGAAGAAACTAAACACACTT
CACTTCTCCCTGATAGAAAGACGTGGGATCAACTGGAGTATTATTTTCCAACCTATGAAAACGACACTCTCCTGTGTACA
CTGTCTGACAGTGAAAGTGACCTGACAGCTCAAGAACAAAATGAGGATGTTCCCATCATCAGTGAAGATACATCTAAACT
GTATGCTTTGAAACAAAGCAGTATTTTGAACCAGTTGCTACTACAA

Alignment

ORF - retro_cjac_558 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.32 %
• Parental protein coverage: 98. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VARLEEDRDGSCSTVGGVGYGDSKDCILEPLSLPESPGGTTTLEGSPSVPCIFCEEHFHVAEQDKLLKHM
          VARLEEDRDGSCSTVGGVGYGDSKDCILEPLSLPESPGGTTTLEGSPSVP.IFCEEHFHVAEQDKLLKHM
Retrocopy VARLEEDRDGSCSTVGGVGYGDSKDCILEPLSLPESPGGTTTLEGSPSVPFIFCEEHFHVAEQDKLLKHM

Parental  IIEHKIVIADVKLVADFQRYILYWRKRFTEQPITDFCSVIRINSTAPFEEQENYFLLCDVLPEDRILREE
          IIEHKIVIADVKLVADFQRYILYWRKRFTEQPITDFCSVIRINSTAPFEEQENYFLLCDVLPEDRILREE
Retrocopy IIEHKIVIADVKLVADFQRYILYWRKRFTEQPITDFCSVIRINSTAPFEEQENYFLLCDVLPEDRILREE

Parental  LQKQKLKEILEQQQQERNDNNFHGICMFCNEEFLGNRSVLLNHMAREHAFNIGLPDNIVNCNEFLCTLQK
          LQKQKLKEILEQQQQERNDNNFHGICMFCNEEFLGNRSVLLNHMAREHAFNIGLPDNIVNCNEFLCTLQK
Retrocopy LQKQKLKEILEQQQQERNDNNFHGICMFCNEEFLGNRSVLLNHMAREHAFNIGLPDNIVNCNEFLCTLQK

Parental  KLDNLQCLYCEKTFRDKNTLKDHMRKKQHRKINPKNREYDRFYVINYLELGKSWEEVQLEDDRELLDNQE
          KLDNLQCLYCEKTFRDKNTLKDHMRKKQ.RKINPKNREYDRFYVINYLELGKSWEEVQLEDDRELLDNQE
Retrocopy KLDNLQCLYCEKTFRDKNTLKDHMRKKQQRKINPKNREYDRFYVINYLELGKSWEEVQLEDDRELLDNQE

Parental  DDWSDWEEHPASAVCLFCEKQAETIEKLYVHMEDAHEFNLLKIKSELGLNFYQQVKLVNFIRRQVHQCRC
          DDWSDWEEHPASAVCLFCEKQAETIEKLYVHMEDA.EFNLLKIKSELGLNFYQQVKLVNFIRRQVHQCRC
Retrocopy DDWSDWEEHPASAVCLFCEKQAETIEKLYVHMEDANEFNLLKIKSELGLNFYQQVKLVNFIRRQVHQCRC

Parental  YGCHVKFKSKADLRTHMEETKHTSLLPDRKTWDQLEYYFPTYENDTLLCTLSDSESDLTAQEQNEDVPII
          YGCHVKFKSKADLRTHMEETKHTSLLPDRKTWDQLEYYFPTYENDTLLCTLSDSESDLTAQEQNEDVPII
Retrocopy YGCHVKFKSKADLRTHMEETKHTSLLPDRKTWDQLEYYFPTYENDTLLCTLSDSESDLTAQEQNEDVPII

Parental  SEDTSKLYALKQSSILNQLLLQ
          SEDTSKLYALKQSSILNQLLLQ
Retrocopy SEDTSKLYALKQSSILNQLLLQ

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	0.60 RPM	6.79 RPM
SRP051959_heart	1.09 RPM	9.79 RPM
SRP051959_kidney	1.02 RPM	15.18 RPM
SRP051959_liver	1.49 RPM	15.05 RPM
SRP051959_lung	0.76 RPM	13.83 RPM
SRP051959_lymph_node	0.75 RPM	7.49 RPM
SRP051959_skeletal_muscle	0.59 RPM	9.06 RPM
SRP051959_spleen	1.01 RPM	12.54 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_558 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_558 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_558 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016891	2 retrocopies	retro_cjac_558 , retro_cjac_698,
Mus musculus	ENSMUSG00000055917	1 retrocopy	retro_mmus_3684,
Otolemur garnettii	ENSOGAG00000005326	1 retrocopy	retro_ogar_1774,