RetrogeneDB ID: retro_cjac_206

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:87360285..87360981(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000033714
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TPM4
• Ensembl ID: ENSCJAG00000014135
• Aliases: None
• Description: tropomyosin 4 [Source:HGNC Symbol;Acc:12013]

Sequence

>retro_cjac_206
CGCCCGCCGCAGATGGTGAAACGCAAGATTCGGGCCCTACAGCAGCAGGCGGAAGAGGCAAAGACCGCGCGCAGGGCCTG
TAACTGCAGCTGGATGGCGGGCGCGAGCGAGCGACTCGAGGAAGCTGAAGGTGATGTGGCTGTCCTCAACCGACGCCTAC
TAGTGGTCATGGCCCTGCAGAAGCTGGAGGAGGCGGGAACGGCTGCAGATGAGCGTGAGAGAGGAATGCAGGTGACAGAA
AACCGGGCCATGACGGATGAGAAGATGGAGATTCAGGAAATGCAGCTCCAAGAGGCCAGGCACACTCTGGAAGGGGCTGA
CCGCAGGTACAAGGAGATAGCTCGAAAGCTGGCCATCCTGGAGGGCGAACTGGCCAGGGAAGAGGAGCGTGTGGAGCTGT
GTGAACGAAAATGTGGTGACCTGGCAGAAGAACTCAAGAATGTCATTAATTATTTGAAATCGCCGGAGGCTGCATCTGAA
AAGTATTCTGAGGAGGACAAATATGAAGAAAAAATTAAACGTCTGTCTGGCAAACTGAAGGAGGCTGAGAACCTTGCTAC
ATTTGCAGAGAGAATGGTTGCAAAACTGGAAGAGACAATTGATGACCTGGAAGAGAAACTTGACCAGGCCAAAGAAGAGA
GCGTGGCCTTCTATCAGACACTGGCTCAGGCACAAAACGAACTTGACTGTATATAA

Alignment

ORF - retro_cjac_206 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.81 %
• Parental protein coverage: 96.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAALNRRIQLVEEELDRAQERLAT--ALQKLEEAEKAADESERGMKVIENRAMKDEEKMEIQEMQLKEAK
          .A....R....E........RL....ALQKLEEA..AADE.ERGM.V.ENRAM.D.EKMEIQEMQL.EA.
Retrocopy MAGASERLEEAEGDVAVLNRRLLVVMALQKLEEAGTAADERERGMQVTENRAMTD-EKMEIQEMQLQEAR

Parental  HIAEEADRKYEEVARKLVILEGELERAEERAEVSELKCGDLEEELKNVTNNLKSLEAASEKYSEKEDKYE
          H..E.ADR.Y.E.ARKL.ILEGEL.R.EER.E..E.KCGDL.EELKNV.N.LKS.EAASEKYSE.EDKYE
Retrocopy HTLEGADRRYKEIARKLAILEGELAREEERVELCERKCGDLAEELKNVINYLKSPEAASEKYSE-EDKYE

Parental  EEIKLLSDKLKEAETRAEFAERTVAKLEKTIDDLEDELYAQKLKYKAISEELDHALNDM
          E.IK.LS.KLKEAE..A.FAER.VAKLE.TIDDLE..L...K....A....L..A.N..
Retrocopy EKIKRLSGKLKEAENLATFAERMVAKLEETIDDLEEKLDQAKEESVAFYQTLAQAQNEL

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	49.10 RPM
SRP051959_heart	0.02 RPM	27.54 RPM
SRP051959_kidney	0.00 RPM	11.43 RPM
SRP051959_liver	0.28 RPM	3.86 RPM
SRP051959_lung	0.00 RPM	40.60 RPM
SRP051959_lymph_node	0.00 RPM	21.85 RPM
SRP051959_skeletal_muscle	0.02 RPM	9.54 RPM
SRP051959_spleen	0.02 RPM	26.09 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_206 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_206 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_206 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_609
Pongo abelii	retro_pabe_624

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004553	2 retrocopies	retro_btau_1604, retro_btau_1758,
Canis familiaris	ENSCAFG00000015796	1 retrocopy	retro_cfam_2107,
Callithrix jacchus	ENSCJAG00000004355	2 retrocopies	retro_cjac_2200, retro_cjac_691,
Callithrix jacchus	ENSCJAG00000009627	2 retrocopies	retro_cjac_1839, retro_cjac_1894,
Callithrix jacchus	ENSCJAG00000009747	9 retrocopies	retro_cjac_1232, retro_cjac_1509, retro_cjac_1580, retro_cjac_1910, retro_cjac_2476, retro_cjac_3121, retro_cjac_527, retro_cjac_785, retro_cjac_798,
Callithrix jacchus	ENSCJAG00000014135	1 retrocopy	retro_cjac_206 ,
Homo sapiens	ENSG00000167460	2 retrocopies	retro_hsap_2623, retro_hsap_3969,
Gorilla gorilla	ENSGGOG00000014510	4 retrocopies	retro_ggor_1836, retro_ggor_2665, retro_ggor_2801, retro_ggor_609,
Monodelphis domestica	ENSMODG00000014882	1 retrocopy	retro_mdom_1354,
Mus musculus	ENSMUSG00000031799	1 retrocopy	retro_mmus_1625,
Nomascus leucogenys	ENSNLEG00000005413	2 retrocopies	retro_nleu_1952, retro_nleu_469,
Oryctolagus cuniculus	ENSOCUG00000009884	1 retrocopy	retro_ocun_1652,
Pan troglodytes	ENSPTRG00000010637	10 retrocopies	retro_ptro_1002, retro_ptro_1109, retro_ptro_1341, retro_ptro_1342, retro_ptro_1750, retro_ptro_1768, retro_ptro_2648, retro_ptro_2694, retro_ptro_2830, retro_ptro_516,
Pteropus vampyrus	ENSPVAG00000009755	2 retrocopies	retro_pvam_186, retro_pvam_187,
Ictidomys tridecemlineatus	ENSSTOG00000024252	1 retrocopy	retro_itri_1858,
Tupaia belangeri	ENSTBEG00000012927	7 retrocopies	retro_tbel_1435, retro_tbel_2468, retro_tbel_3663, retro_tbel_3709, retro_tbel_3872, retro_tbel_4651, retro_tbel_482,
Tarsius syrichta	ENSTSYG00000010642	9 retrocopies	retro_tsyr_1377, retro_tsyr_1613, retro_tsyr_1642, retro_tsyr_1853, retro_tsyr_628, retro_tsyr_694, retro_tsyr_704, retro_tsyr_742, retro_tsyr_749,
Tursiops truncatus	ENSTTRG00000014542	2 retrocopies	retro_ttru_504, retro_ttru_839,