RetrogeneDB ID: retro_cjac_2784

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:3898244..3898907(-)
• Located in intron of: ENSCJAG00000011798

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000019406
• Aliases: None
• Description: None

Sequence

>retro_cjac_2784
ATGGGGCTGTTGGTTAAAACCCAGGAGAAGCCACCAAAAGAACTGGCCAATGAATGGTCATTGAAGATAAGAAAGGAAAT
GAGAGTTGTTGACAGGCAAATAAAGGATATCCAAAGAGAAGAAGAAAAAGTGAAATGATCTGTGAAAGATGCAGTCAAGA
AGGGCCAGAAGGAAATGTGCACGGTTCTGGCCAGGGAGATGATCAGGTCAGGGAAGGCCGCGAGCAAGCTGTATGCATCC
AAAGCGCCCATGAACTCAGTGCTCATGGGGATGAGGAACCAGCTTGCGGTCTTGCGAGTGGCTGGTTCCCTGTAGAAGAG
CACAGAAGTGATGAGGGCCATGCAGAGTCTTGTGAAGATTCCAGAAATTCAGGCCACCATGAGGGAGCTGTCCAAAGAAA
TGATGAAGGCTGGGATCATAGAGGAGATGTTAGAGGACACTTTCGAAAGCGTGGACGATCAGGAAGAAATGGAGGAAGAA
GCAGAAATGGAAATTGACAAAATTCTATTTGAAATTACAGCAGGGGCCTTGGGCAAAGCACCCAGTAAAGTGACTGATGC
TCTTCCAGAGCCAGAACCTTCAGGAGCGATGGCTGCCCCAGAGGATGAGGAGGAGGAAGAAGCTCTGGGGGCCATGCAGT
CCCGGCTGGCCACACTCCACAGC

Alignment

ORF - retro_cjac_2784 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGLFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCVVLAKEMIRS
          MGL..KTQEKPPKEL.NEWSLKIRKEMRVVDRQI.DIQREEEKVK.SVKDA.KKGQK..C.VLA.EMIRS
Retrocopy MGLLVKTQEKPPKELANEWSLKIRKEMRVVDRQIKDIQREEEKVK*SVKDAVKKGQKEMCTVLAREMIRS

Parental  RKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMRELSKEMMKAGII
          .KA.SKLYASKA.MNSVLMGM.NQLAVLRVAGSL.KSTEVM.AMQSLVKIPEIQATMRELSKEMMKAGII
Retrocopy GKAASKLYASKAPMNSVLMGMRNQLAVLRVAGSL*KSTEVMRAMQSLVKIPEIQATMRELSKEMMKAGII

Parental  EEMLEDTFESMDDQEEMEEEAEMEIDKILFEITAGALGKAPSKVTDALPEPEPSGAMAPSEDEEEEEALE
          EEMLEDTFES.DDQEEMEEEAEMEIDKILFEITAGALGKAPSKVTDALPEPEPSGAMA..EDEEEEEAL.
Retrocopy EEMLEDTFESVDDQEEMEEEAEMEIDKILFEITAGALGKAPSKVTDALPEPEPSGAMAAPEDEEEEEALG

Parental  AMQSRLATLRS
          AMQSRLATL.S
Retrocopy AMQSRLATLHS

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	1.66 RPM	31.42 RPM
SRP051959_heart	1.11 RPM	29.06 RPM
SRP051959_kidney	1.46 RPM	34.23 RPM
SRP051959_liver	0.80 RPM	18.65 RPM
SRP051959_lung	1.95 RPM	28.70 RPM
SRP051959_lymph_node	1.89 RPM	16.76 RPM
SRP051959_skeletal_muscle	1.11 RPM	21.07 RPM
SRP051959_spleen	1.95 RPM	29.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2784 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2784 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2784 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007479	1 retrocopy	retro_cfam_1869,
Callithrix jacchus	ENSCJAG00000019406	2 retrocopies	retro_cjac_2032, retro_cjac_2784 ,
Cavia porcellus	ENSCPOG00000001723	1 retrocopy	retro_cpor_920,
Macropus eugenii	ENSMEUG00000009111	1 retrocopy	retro_meug_178,
Microcebus murinus	ENSMICG00000005492	3 retrocopies	retro_mmur_1110, retro_mmur_1396, retro_mmur_47,
Mus musculus	ENSMUSG00000053119	1 retrocopy	retro_mmus_1683,
Oryctolagus cuniculus	ENSOCUG00000029277	1 retrocopy	retro_ocun_1044,
Ochotona princeps	ENSOPRG00000002191	2 retrocopies	retro_opri_18, retro_opri_436,
Sorex araneus	ENSSARG00000008917	1 retrocopy	retro_sara_13,
Tursiops truncatus	ENSTTRG00000010400	1 retrocopy	retro_ttru_638,