RetrogeneDB ID: retro_cjac_2238

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:64451801..64452593(-)
• Located in intron of: ENSCJAG00000003278

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENO1
• Ensembl ID: ENSCJAG00000000359
• Aliases: None
• Description: None

Sequence

>retro_cjac_2238
ATCCTCCCAGTGGGTGCCGCAAACTTCAGGGAAGCCATGCGCATCGGAGCGGAGGTTTACCACAACCTGAAGAACGTCAA
GGAGAAATACGGGAAAGATGCCACCAATGTGGGCGATGAAGGCGGGTTTGCTCCCAACATCCTAGAGAATAAAGAAGGCC
TGGAGCTGCTGAAGACTGCAATTGGGAAAGCTGGCTACACCGATAAGGTGGTCATCGGCATGGATGTGGCAGCCTCTGAG
TTCTACAGGTCTGGGAAGTATGACCTGGATTTCAAGTCTCCTGATGATCCCAGCAGGTACATCTCACCTGACCAGCTGGC
CGACCTGTACAAGTCCTTCATCAAGGACTACCCAGTGGTGTCTATCGAAGATCCCTTTGACCAGAATGACTGGGGAGCAT
GGAAGAACTTCACAGCCAGTGAAGGAATCCAGGTGGTGGGGGATGATCTCACAGTGACCAACCCGAAAAGGATTGCCAAG
GCTGCAAATGAGAAGTCCTGCAACTGCCTGCTGCTCAAAGTGAACCAGATCGGCTCTGTGACCGAGTCCCTGCAGGTGTG
CAAGTTGGCCCAGGCCAATGGTTGGGGCGTCATGGTGTCTCATCGTTCTGGGGAGACTGAAGATACCTTCATCGCCGACC
TGGTGGTGGGGCTGTGCACTGGGCAGATCAAGACTGGTGCCCCTTGCCGATCTGAGCGCTTGGCCAAGTACAACCAGCTC
CTCAGAATTGAAGAGGAGCTGGGCAGCAAGGCCAAGTTTGCTGGCAGGAACTTCAGAAACCCCCTGGCCAAG

Alignment

ORF - retro_cjac_2238 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.74 %
• Parental protein coverage: 61.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILPVGAANFREAMRIGAEVYHNLKNVIKEKYGKDATNVGDEGGFAPNILENKEGLELLKTAIGKAGYTDK
          ILPVGAANFREAMRIGAEVYHNLKNV.KEKYGKDATNVGDEGGFAPNILENKEGLELLKTAIGKAGYTDK
Retrocopy ILPVGAANFREAMRIGAEVYHNLKNV-KEKYGKDATNVGDEGGFAPNILENKEGLELLKTAIGKAGYTDK

Parental  VVIGMDVAASEFYRSGKYDLDFKSPDDPSRYISPDQLADLYKSFIKDYPVVSIEDPFDQDDWGAWQKFTA
          VVIGMDVAASEFYRSGKYDLDFKSPDDPSRYISPDQLADLYKSFIKDYPVVSIEDPFDQ.DWGAW..FTA
Retrocopy VVIGMDVAASEFYRSGKYDLDFKSPDDPSRYISPDQLADLYKSFIKDYPVVSIEDPFDQNDWGAWKNFTA

Parental  SAGIQVVGDDLTVTNPKRIAKAANEKSCNCLLLKVNQIGSVTESLQACKLAQANGWGVMVSHRSGETEDT
          S.GIQVVGDDLTVTNPKRIAKAANEKSCNCLLLKVNQIGSVTESLQ.CKLAQANGWGVMVSHRSGETEDT
Retrocopy SEGIQVVGDDLTVTNPKRIAKAANEKSCNCLLLKVNQIGSVTESLQVCKLAQANGWGVMVSHRSGETEDT

Parental  FIADLVVGLCTGQIKTGAPCRSERLAKYNQLLRIEEELGSKAKFAGRNFRNPLAK
          FIADLVVGLCTGQIKTGAPCRSERLAKYNQLLRIEEELGSKAKFAGRNFRNPLAK
Retrocopy FIADLVVGLCTGQIKTGAPCRSERLAKYNQLLRIEEELGSKAKFAGRNFRNPLAK

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	0.20 RPM	148.77 RPM
SRP051959_heart	0.05 RPM	85.02 RPM
SRP051959_kidney	0.18 RPM	148.18 RPM
SRP051959_liver	0.13 RPM	188.84 RPM
SRP051959_lung	0.24 RPM	50.46 RPM
SRP051959_lymph_node	0.21 RPM	86.37 RPM
SRP051959_skeletal_muscle	0.07 RPM	45.75 RPM
SRP051959_spleen	0.23 RPM	67.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2238 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2238 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2238 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003483	2 retrocopies	retro_chof_1289, retro_chof_1811,
Callithrix jacchus	ENSCJAG00000000359	4 retrocopies	retro_cjac_1963, retro_cjac_2238 , retro_cjac_3891, retro_cjac_438,
Callithrix jacchus	ENSCJAG00000011679	2 retrocopies	retro_cjac_115, retro_cjac_177,
Erinaceus europaeus	ENSEEUG00000008602	2 retrocopies	retro_eeur_23, retro_eeur_243,
Homo sapiens	ENSG00000074800	1 retrocopy	retro_hsap_325,
Macropus eugenii	ENSMEUG00000005942	11 retrocopies	retro_meug_1445, retro_meug_1521, retro_meug_353, retro_meug_472, retro_meug_494, retro_meug_652, retro_meug_664, retro_meug_765, retro_meug_794, retro_meug_874, retro_meug_888,
Macropus eugenii	ENSMEUG00000007840	1 retrocopy	retro_meug_96,
Monodelphis domestica	ENSMODG00000009521	1 retrocopy	retro_mdom_1794,
Mustela putorius furo	ENSMPUG00000006382	2 retrocopies	retro_mputfur_1162, retro_mputfur_547,
Mus musculus	ENSMUSG00000063524	1 retrocopy	retro_mmus_109,
Oryctolagus cuniculus	ENSOCUG00000010086	1 retrocopy	retro_ocun_933,
Otolemur garnettii	ENSOGAG00000004001	1 retrocopy	retro_ogar_1059,
Ochotona princeps	ENSOPRG00000009492	1 retrocopy	retro_opri_969,
Pan troglodytes	ENSPTRG00000000109	1 retrocopy	retro_ptro_261,
Pteropus vampyrus	ENSPVAG00000005030	1 retrocopy	retro_pvam_317,
Rattus norvegicus	ENSRNOG00000017895	1 retrocopy	retro_rnor_112,
Sarcophilus harrisii	ENSSHAG00000005522	1 retrocopy	retro_shar_304,
Tarsius syrichta	ENSTSYG00000002509	1 retrocopy	retro_tsyr_2011,