RetrogeneDB ID: retro_cjac_139

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:39032534..39033659(+)
• Located in intron of: ENSCJAG00000019620

Retrocopy information

• Ensembl ID: ENSCJAG00000022821
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ACTG1
• Ensembl ID: ENSCJAG00000002885
• Aliases: None
• Description: actin, gamma 1 [Source:HGNC Symbol;Acc:144]

Sequence

>retro_cjac_139
ATGGAAGAAGAAATTGCTGCGCTCGTCATCGACAATGGTTCCGGCATGTGCAAAGCTGGCTTTGCTGGGGACGACGCCCC
CCGAGCCGTGTTTCCCTCCATTGTCGGGCGCCCTCGGCACCAGGGCGTGATGGTCGGCATGGGCCAGAAGGACTCCTACG
TGGGCGACGAGGCCCAGAGCAAGCGCGGCATCCTGACCCTGAAGTACCCCATCGAGCACATCGTCACCAATTGGGATGAT
ATGGAGAAAATCTGGCACCACACTTTTTACAATGAGTTGCGTGTGGCCCCGGAGGAGCACCCCGTGTTGCTGACCGAGGC
CCCCCTGAACCCCAAGGCCAACAAAGAGAAGATGACTCAGATCATGTTTGAGACCTTCAACACCCCAGCCATGTACGTGG
CTATCCAGGCCGTGCTGTCCCTCTATGCCTCTGGGCGCACCACTGGTATTGTCATGGACTCTGGAGATGGGGTAACCCAC
ACGGTGCCCATTTACGAGGGCTATGCCCTTCCACATGCTATCCTGCATCTGGACCTGGCTGGCCGGGACCTGACCGACTA
CCTCATGAAGATCCTCACGGAACGCGGCTACAGCTTCACCACCACGGCCAAGCGGGAGATCGTACGCGACATCAAGGAGA
AGCTGTGCTATGTTGCCCTGGACTTCAAGCAGGAGATGGCCACAGCTGCATCCTCCTCCTCTCTGGAGAAGAGCTATGAG
CTGCCTGACGGCCAGGTCATCACCATTGGTAACGAGCAGTTCCGGTGTCCGGAGGCGCTGTTCCAGCCTTCCTTTCTTGG
CATGGAATCTTGTGGCATCCATGAGACCACCTTCAACTCCATCATGAAGTGTGACGTGGACATCCGCAAAGACCTGTACG
CCAACACTGTGCTGTCTGGCGGCACCACTATGTACCCAGGCATCGCCGACAGGATGCAGAAGGAGATCACTGCTCTTGCG
CCCAGCACCATGAAGATCAAGATCATTGCACCCCCAGAGCATAAGTACTCCGTGTGGATCGGCGGCTCCATCCTGGCCTC
ACTGTCCACCTTCCAACAGATGTGGATTAGCAAGCAGGAGTACGATGAGTCTGGCCCCTCCATCGTCCACCGCAAATGCT
TCTAA

Alignment

ORF - retro_cjac_139 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.13 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
          MEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
Retrocopy MEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP

Parental  IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
          IEH.IVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKAN.EKMTQIMFETFNTPAMYVAIQAVL
Retrocopy IEH-IVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANKEKMTQIMFETFNTPAMYVAIQAVL

Parental  SLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR
          SLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAIL.LDLAGRDLTDYLMKILTERGYSFTTTA.REIVR
Retrocopy SLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILHLDLAGRDLTDYLMKILTERGYSFTTTAKREIVR

Parental  DIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN
          DIKEKLCYVALDF.QEMATAASSSSLEKSYELPDGQVITIGNE.FRCPEALFQPSFLGMESCGIHETTFN
Retrocopy DIKEKLCYVALDFKQEMATAASSSSLEKSYELPDGQVITIGNEQFRCPEALFQPSFLGMESCGIHETTFN

Parental  SIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLS
          SIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPE.KYSVWIGGSILASLS
Retrocopy SIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPEHKYSVWIGGSILASLS

Parental  TFQQMWISKQEYDESGPSIVHRKCF
          TFQQMWISKQEYDESGPSIVHRKCF
Retrocopy TFQQMWISKQEYDESGPSIVHRKCF

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	0.51 RPM	295.29 RPM
SRP051959_heart	0.18 RPM	104.00 RPM
SRP051959_kidney	0.33 RPM	203.34 RPM
SRP051959_liver	0.13 RPM	112.98 RPM
SRP051959_lung	0.23 RPM	157.88 RPM
SRP051959_lymph_node	0.30 RPM	162.60 RPM
SRP051959_skeletal_muscle	0.09 RPM	93.38 RPM
SRP051959_spleen	0.02 RPM	124.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_139 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_139 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 30 parental genes, and 147 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015238	3 retrocopies	retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca	ENSAMEG00000016015	1 retrocopy	retro_amel_929,
Bos taurus	ENSBTAG00000006189	2 retrocopies	retro_btau_286, retro_btau_903,
Callithrix jacchus	ENSCJAG00000000008	2 retrocopies	retro_cjac_243, retro_cjac_56,
Callithrix jacchus	ENSCJAG00000002885	3 retrocopies	retro_cjac_139 , retro_cjac_336, retro_cjac_377,
Cavia porcellus	ENSCPOG00000012101	1 retrocopy	retro_cpor_361,
Equus caballus	ENSECAG00000018600	1 retrocopy	retro_ecab_98,
Felis catus	ENSFCAG00000026434	2 retrocopies	retro_fcat_257, retro_fcat_377,
Homo sapiens	ENSG00000184009	10 retrocopies	retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus	ENSGALG00000028749	1 retrocopy	retro_ggal_6,
Gorilla gorilla	ENSGGOG00000014043	6 retrocopies	retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Macropus eugenii	ENSMEUG00000016247	57 retrocopies	retro_meug_1006, retro_meug_1010, retro_meug_1018, retro_meug_1042, retro_meug_105, retro_meug_1085, retro_meug_1147, retro_meug_1186, retro_meug_1200, retro_meug_1230, retro_meug_1237, retro_meug_1380, retro_meug_1414, retro_meug_1437, retro_meug_1529, retro_meug_1534, retro_meug_1557, retro_meug_1588, retro_meug_1613, retro_meug_1624, retro_meug_1654, retro_meug_1656, retro_meug_1664, retro_meug_1669, retro_meug_1708, retro_meug_1716, retro_meug_1723, retro_meug_1753, retro_meug_1763, retro_meug_18, retro_meug_1935, retro_meug_1969, retro_meug_197, retro_meug_1982, retro_meug_1991, retro_meug_2100, retro_meug_2176, retro_meug_218, retro_meug_270, retro_meug_333, retro_meug_370, retro_meug_379, retro_meug_468, retro_meug_506, retro_meug_556, retro_meug_574, retro_meug_581, retro_meug_61, retro_meug_735, retro_meug_790, retro_meug_833, retro_meug_90, retro_meug_900, retro_meug_915, retro_meug_924, retro_meug_925, retro_meug_959,
Microcebus murinus	ENSMICG00000014863	3 retrocopies	retro_mmur_23, retro_mmur_352, retro_mmur_6,
Monodelphis domestica	ENSMODG00000002647	3 retrocopies	retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furo	ENSMPUG00000011610	1 retrocopy	retro_mputfur_279,
Mus musculus	ENSMUSG00000062825	7 retrocopies	retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys	ENSNLEG00000013385	15 retrocopies	retro_nleu_1008, retro_nleu_1058, retro_nleu_1059, retro_nleu_1150, retro_nleu_1347, retro_nleu_1474, retro_nleu_1729, retro_nleu_2193, retro_nleu_2393, retro_nleu_2574, retro_nleu_2669, retro_nleu_3032, retro_nleu_344, retro_nleu_813, retro_nleu_974,
Nomascus leucogenys	ENSNLEG00000015506	3 retrocopies	retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Oryctolagus cuniculus	ENSOCUG00000005867	1 retrocopy	retro_ocun_720,
Otolemur garnettii	ENSOGAG00000008040	3 retrocopies	retro_ogar_148, retro_ogar_1808, retro_ogar_2430,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pongo abelii	ENSPPYG00000008735	11 retrocopies	retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pelodiscus sinensis	ENSPSIG00000002102	2 retrocopies	retro_psin_25, retro_psin_4,
Rattus norvegicus	ENSRNOG00000036701	1 retrocopy	retro_rnor_715,
Sorex araneus	ENSSARG00000012197	1 retrocopy	retro_sara_267,
Sus scrofa	ENSSSCG00000028355	1 retrocopy	retro_sscr_389,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Tupaia belangeri	ENSTBEG00000010781	1 retrocopy	retro_tbel_422,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,