RetrogeneDB ID: retro_cjac_2186

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:136907702..136908665(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A33
• Ensembl ID: ENSCJAG00000000424
• Aliases: None
• Description: None

Sequence

>retro_cjac_2186
ATGGCGACCGACGGCCGGCAGAAGGAGAACACGCTGCTTCACCTCTTCGCCGGCGGGGGCGGAGGCACAGTTGGTGCCAT
TTTCACTTGTCCACTAGAAGTCATTAAGACGCGGTTGCAGTCTTCGAGATTAGCCCTCCGGACAGTCTACTATCCTCAGG
TTCATCTGGGGACCATTAGTGGAGCTGGAATGGTGAGACCAACATCCGTGACACCTGGACTCTTTCCGGTTCTGAAGCCG
ATCTTGGAGAAAGAGGGACCAAAGTCACTTTTTAGAGGCTTGGGTCCAAATTTGGTTGGAGCTGCACCGTGAAGGGCTGT
ATACTTTGCATGTTACTCCAAAGCCAAAGAGCAATTTAATGGCATTTTCATGCCTAACAGCAATATTGTGCATATTTTCT
CAGCTGACTCTGCAGCTTTTATCACAAATTCCTTAATGAATCCTATATGGATGGTTAAAACCCGAATGCAGCTAGAACGA
AAAGTGAGGGGCTCTAAGCAGACGAATACACTCCAGTGTGCTTGCTACGTTTACCAGACCGAAGGAATTCATGACTTCTA
CAGAGGATTAACTGCCTCGTATGCTGGAATTTCCGAAACGAAAATCTGCTTTGCTTTTTATGAAAGTTTAAAGAAGTATC
TGAAAGAAACTTCATTAGCCTCTTTGCAAATGCGACTGAGAAAAATTCCACAGGTTTTTTTGGTTCTTATGGCAGCTGCT
GCTCTTTCTAAGGGCTGTGCCTCCTGCATTGCTTATCCACACGAGGTCATAAGGACGAGGCTCCGGGAGGAGGGCACCAA
GTACAAGTCCTTTGTCCAGACGGCGCGCCTGGTGTTCCGGGAAGAAGGCTACCTCGCCTTCTATAAAGCACTCTTCGCCC
AGCTCATCCGGCAGATCCCAAATACTGCCACTGTGTTGTCTACTTACAAGTTAATTGTGTACCTGTTAGAAGACCGTATT
CAG

Alignment

ORF - retro_cjac_2186 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.95 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATDGRQKENTLLHLFAGGCGGTVGAIFTCPLEVIKTRLQSSRLALRTVYYPQVHLGTISGAGMVRPTSV
          MATDGRQKENTLLHLFAGG.GGTVGAIFTCPLEVIKTRLQSSRLALRTVYYPQVHLGTISGAGMVRPTSV
Retrocopy MATDGRQKENTLLHLFAGGGGGTVGAIFTCPLEVIKTRLQSSRLALRTVYYPQVHLGTISGAGMVRPTSV

Parental  TPGLFQVLKSILEKEGPKSLFRGLGPNLVGVAPSRAVYFACYSKAKEQFNGIFVPNSNIVHIFSAGSAAF
          TPGLF.VLK.ILEKEGPKSLFRGLGPNLVG.AP.RAVYFACYSKAKEQFNGIF.PNSNIVHIFSA.SAAF
Retrocopy TPGLFPVLKPILEKEGPKSLFRGLGPNLVGAAP*RAVYFACYSKAKEQFNGIFMPNSNIVHIFSADSAAF

Parental  ITNSLMNPIWMVKTRMQLEQKVRGSKQMNTLQCARYVYRTEGIRGFYRGLTASYAGISETIICFAIYESL
          ITNSLMNPIWMVKTRMQLE.KVRGSKQ.NTLQCA.YVY.TEGI..FYRGLTASYAGISET.ICFA.YESL
Retrocopy ITNSLMNPIWMVKTRMQLERKVRGSKQTNTLQCACYVYQTEGIHDFYRGLTASYAGISETKICFAFYESL

Parental  KKYLKEAPLAS-SANGTEKNSTGFFG-LMAAAALSKGCASCIAYPHEVIRTRLREEGTKYKSFVQTARLV
          KKYLKE..LAS..AN.TEKNSTGFFG.LMAAAALSKGCASCIAYPHEVIRTRLREEGTKYKSFVQTARLV
Retrocopy KKYLKETSLAS<FANATEKNSTGFFG>LMAAAALSKGCASCIAYPHEVIRTRLREEGTKYKSFVQTARLV

Parental  FREEGYLAFYRGLFAQLIRQIPNTAIVLSTYELIVYLLEDRTQ
          FREEGYLAFY..LFAQLIRQIPNTA.VLSTY.LIVYLLEDR.Q
Retrocopy FREEGYLAFYKALFAQLIRQIPNTATVLSTYKLIVYLLEDRIQ

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	4.13 RPM
SRP051959_heart	0.00 RPM	3.60 RPM
SRP051959_kidney	0.02 RPM	9.14 RPM
SRP051959_liver	0.00 RPM	10.90 RPM
SRP051959_lung	0.00 RPM	1.89 RPM
SRP051959_lymph_node	0.00 RPM	3.61 RPM
SRP051959_skeletal_muscle	0.02 RPM	4.61 RPM
SRP051959_spleen	0.00 RPM	1.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2186 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2186 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2186 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000424	1 retrocopy	retro_cjac_2186 ,
Dasypus novemcinctus	ENSDNOG00000014396	1 retrocopy	retro_dnov_2369,
Homo sapiens	ENSG00000171612	1 retrocopy	retro_hsap_873,
Gorilla gorilla	ENSGGOG00000006766	1 retrocopy	retro_ggor_709,
Monodelphis domestica	ENSMODG00000003059	1 retrocopy	retro_mdom_1512,
Otolemur garnettii	ENSOGAG00000007103	1 retrocopy	retro_ogar_2098,