RetrogeneDB ID: retro_cjac_3023

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:128099483..128100539(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021839
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000005910
• Aliases: None
• Description: None

Sequence

>retro_cjac_3023
ATGGTGTCCCGCAAGGAAGGTACCGGCTCTTCTGCCACCTCTTCCAGTTCCACCGCCGGCGCAGCAGGGAAAGGCAAAGG
CAAAGGCGGCTCTGGAGATTCAGCCGTGAAGCAAGTGCAGATAGATGGCCTTGTGGTATTAAAGATAATCAAACATTATC
AAGAAGAAGGACAAGGAACTGAAGTTGTTCAAGGAGTGCTTTTGGGCCTGGTTGTAGAAGATCGGCTTGAAATTACCAAC
TGCTTTCCCTTCCCTCAGCACACAGAGGATGATGCTGACTTTGATGAAGTCCAATATCAGATGGAAATGATGCGGAGCCT
TCGCCATGTAAACATTGATCATCTTCATGTGGGCCGGTACCAGTCCACATACTATGGCTCATTTGTCACCCGAGCGCTCC
TGGACTCTCAGTTCAGTTACCAGCATGCCATTGAAGAATCTGTCGTTCTCATTTATGATCCCATAAAAACTGCCCAAGGG
TCTCTCTCACTAAAGGCATACAGACTGACTCCTAAACTGATGGAAGTTTGTAAAGAGAAGGATTTTTCCCCTGAAGCATT
GAAAAAAGCAAATATCACCTTTGAGTACATGTTTGAAGAAGTGCCGATTGTAATTAAAAATTCACATCTGATTAATGTCT
TAATGTGGGAACTTGAAAAGAAGTCAGCTGTAGCAGATAAACATGAATTGCTCAGCCTTGCCAGCAGCAATCATTTGGGG
AAGAATCTACAGTTGCTGATGGACAGAGTGGACGAAATGAGCCAGGATATAGTTAAATACAACACATACATGAGGAATAC
TAGTAAACAGCAGCAGCAGAAACATCAGTATCAGCAGCATGGCCAGCAAGAGAATATGCAGCGCCAGAGCCGAGGAGAAC
CCCCGCTCCCTGAGGAGAACCTGTCCAAACTCTTCAAACCACCACAGCCTCCTGCCAGGATGGACTCACTGCTCATTGCA
GGCCAGATAAACACTTACTGCCAGAACATCAAGGAGTTCACTGCCCAAAACTTAGGCAAGCTCTTCATGGCCCAGGCTCT
TCAAGAATACAACAAC

Alignment

ORF - retro_cjac_3023 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.58 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASRKEGTGSSATSSSSTAGAAGKGKGKGGSGDSAVKQVQIDGLVVLKIIKHYQEEGQGTEVVQGVLLGL
          M.SRKEGTGSSATSSSSTAGAAGKGKGKGGSGDSAVKQVQIDGLVVLKIIKHYQEEGQGTEVVQGVLLGL
Retrocopy MVSRKEGTGSSATSSSSTAGAAGKGKGKGGSGDSAVKQVQIDGLVVLKIIKHYQEEGQGTEVVQGVLLGL

Parental  VVEDRLEITNCFPFPQHTEDDADFDEVQYQMEMMRSLRHVNIDHLHVGWYQSTYYGSFVTRALLDSQFSY
          VVEDRLEITNCFPFPQHTEDDADFDEVQYQMEMMRSLRHVNIDHLHVG.YQSTYYGSFVTRALLDSQFSY
Retrocopy VVEDRLEITNCFPFPQHTEDDADFDEVQYQMEMMRSLRHVNIDHLHVGRYQSTYYGSFVTRALLDSQFSY

Parental  QHAIEESVVLIYDPIKTAQGSLSLKAYRLTPKLMEVCKEKDFSPEALKKANITFEYMFEEVPIVIKNSHL
          QHAIEESVVLIYDPIKTAQGSLSLKAYRLTPKLMEVCKEKDFSPEALKKANITFEYMFEEVPIVIKNSHL
Retrocopy QHAIEESVVLIYDPIKTAQGSLSLKAYRLTPKLMEVCKEKDFSPEALKKANITFEYMFEEVPIVIKNSHL

Parental  INVLMWELEKKSAVADKHELLSLASSNHLGKNLQLLMDRVDEMSQDIVKYNTYMRNTSKQQQQKHQYQQR
          INVLMWELEKKSAVADKHELLSLASSNHLGKNLQLLMDRVDEMSQDIVKYNTYMRNTSKQQQQKHQYQQ.
Retrocopy INVLMWELEKKSAVADKHELLSLASSNHLGKNLQLLMDRVDEMSQDIVKYNTYMRNTSKQQQQKHQYQQH

Parental  RQQENMQRQSRGEPPLPEEDLSKLFKPPQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEY
          .QQENMQRQSRGEPPLPEE.LSKLFKPPQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEY
Retrocopy GQQENMQRQSRGEPPLPEENLSKLFKPPQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEY

Parental  NN
          NN
Retrocopy NN

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	36.68 RPM
SRP051959_heart	0.46 RPM	45.27 RPM
SRP051959_kidney	0.33 RPM	44.04 RPM
SRP051959_liver	0.52 RPM	50.25 RPM
SRP051959_lung	0.29 RPM	48.69 RPM
SRP051959_lymph_node	0.68 RPM	66.23 RPM
SRP051959_skeletal_muscle	0.66 RPM	71.98 RPM
SRP051959_spleen	0.76 RPM	69.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3023 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3023 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3023 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000816	1 retrocopy	retro_cfam_2073,
Callithrix jacchus	ENSCJAG00000005910	1 retrocopy	retro_cjac_3023 ,
Echinops telfairi	ENSETEG00000000324	1 retrocopy	retro_etel_24,
Macropus eugenii	ENSMEUG00000015663	4 retrocopies	retro_meug_1223, retro_meug_1244, retro_meug_1790, retro_meug_376,
Monodelphis domestica	ENSMODG00000004154	1 retrocopy	retro_mdom_1243,
Mus musculus	ENSMUSG00000022312	1 retrocopy	retro_mmus_1668,
Oryctolagus cuniculus	ENSOCUG00000007534	1 retrocopy	retro_ocun_608,
Otolemur garnettii	ENSOGAG00000008905	1 retrocopy	retro_ogar_2043,
Sorex araneus	ENSSARG00000009067	1 retrocopy	retro_sara_69,
Sarcophilus harrisii	ENSSHAG00000014977	1 retrocopy	retro_shar_561,
Ictidomys tridecemlineatus	ENSSTOG00000001403	1 retrocopy	retro_itri_420,