RetrogeneDB ID: retro_cjac_1219

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:69462947..69464178(+)
• Located in intron of: ENSCJAG00000015097

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASS1
• Ensembl ID: ENSCJAG00000020554
• Aliases: None
• Description: None

Sequence

>retro_cjac_1219
ATGTCCAGCAAAGGCTCCGTGGTTCTGGCCTACAGTGGTGGCCTAGATACCTCCTGCATCCTCATTTAACTTAAGGAACA
AGGCTATGATGTCATTGCCCACCTAGCCAACATCGGCCAGAAGGAAGACTTGGAGGAAGCCAGGAAGAAGGCACTGAACC
TTGGGACAAGAAAGGTGTTCATTGAGGATATCAGCAAGGAGTTTGTGGAGAAGTTTATCTGGCTGGCCATCCAGTTCAGT
GCACTGTATGAGGACCACTACCTCCTGGGCACCTCTCTCACTGGCCCCTGCATCACCCGCAAACAAGTGGAAATTGCCCA
GCGGGAGGAGGCCAACTATGTGTCCCACAGTGCCATGGGAAAGGGGAACAATCAGGTCCAGTTTGAGCTCACCTGCTACT
CACTGGGTCCCCAGGTTACGGTCATTGCTCCCTAAAGGATGCCTGAGTTCTACAACCAGTTCAAGGTCTGCAGTGATCTG
ATGAAATACACAAAGAAACATGGCATTCCAATTCCAGTCACTCCAAAGAACCCATGGAGCATGGACGAGAACAGCATGCA
CATCAGCTACGAGACTGGAATCTTGGACAACCCCAAGAACCAAGCACCTTCAGGTCTCTACATGAAGACCCAGGATGAAG
CCAAAGCCCCCAGGACCCCTGACGTTCTCAAGATTGAGTAAAAAAACGGTTTTCCGTGAAGGTGATCAGCATCAAGGATA
GCACCACCTACCAGATCTCCTTGCAGCTCTTCATTTACCTGAACGAAGTCGCAGGCAAGCACAGCGTGGGCCGTATAGAC
ATCGTGGAGAACTGCCTCATGAAATGAACTCCTGAGGTATCTATGGGACCCCAGCAGGCACCATTCTTTACCACCCTCAT
TTAGACATTGAGGCCTTCGCTGTGGACCAGGAAGTGCACAGAATCAAATACGGCCTGGGCTTGAAATTTGCTGAGTTGGT
GTACACCAGTTTCTGGCACAGCCCTGAGTGTAAATTTGCCTGCCACTGCATCTCCAAGTCCTAGGAGCAAGTGGAAGGAA
AAGTGCAGCTGTCCATCTTCAGGGGCCAGGTGTACATCCTCTGCCAGGAGTCCCCACAGTCTCTCTACAATGGGAAGCTG
GTGAGCATGAACATGCAGGGTGATTATGAGCCAATCAGTGCCACCAGCCTCATCAACATCGGTTCCCTCAGGCTGAAGAA
ATACCGTCTCCAGAGCAAGGTCACTGCCAAA

Alignment

ORF - retro_cjac_1219 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSKGSVVLAYSGGLDTSCILVWLKEQGYDVIAYLANIGQKEDFEEARKKALKLGAKKVFIEDVSREFVE
          MSSKGSVVLAYSGGLDTSCIL..LKEQGYDVIA.LANIGQKED.EEARKKAL.LG..KVFIED.S.EFVE
Retrocopy MSSKGSVVLAYSGGLDTSCILI*LKEQGYDVIAHLANIGQKEDLEEARKKALNLGTRKVFIEDISKEFVE

Parental  EFIWPAIQSSALYEDRYLLGTSLARPCIARKQVEIAQREGAKYVSHGATGKGNDQVRFELTCYSLAPQIK
          .FIW.AIQ.SALYED.YLLGTSL..PCI.RKQVEIAQRE.A.YVSH.A.GKGN.QV.FELTCYSL.PQ..
Retrocopy KFIWLAIQFSALYEDHYLLGTSLTGPCITRKQVEIAQREEANYVSHSAMGKGNNQVQFELTCYSLGPQVT

Parental  VIAPWRMPEFYNRFKGRNDLMEYAKQHGIPIPVTPKNPWSMDENLMHISYEAGILENPKNQAPPGLYTKT
          VIAP.RMPEFYN.FK...DLM.Y.K.HGIPIPVTPKNPWSMDEN.MHISYE.GIL.NPKNQAP.GLY.KT
Retrocopy VIAP*RMPEFYNQFKVCSDLMKYTKKHGIPIPVTPKNPWSMDENSMHISYETGILDNPKNQAPSGLYMKT

Parental  QDPAKAPNTPDILEIEFKKGVP-VKVTNVKDGTTHQTSLELFMYLNEVAGKHGVGRIDIVENRFI-GMKS
          QD.AKAP.TPD.L.IE.K.G.P.VKV...KD.TT.Q.SL.LF.YLNEVAGKH.VGRIDIVEN.....M.S
Retrocopy QDEAKAPRTPDVLKIE*KNGFP<VKVISIKDSTTYQISLQLFIYLNEVAGKHSVGRIDIVENCLM<EMNS

Parental  RGIYETPAGTILYHAHLDIEAFTMDREVRKIKQGLGLKFAELVYTGFWHSPECEFVRHCIAKSQERVEGK
          .GIY.TPAGTILYH.HLDIEAF..D.EV..IK.GLGLKFAELVYT.FWHSPEC.F..HCI.KS.E.VEGK
Retrocopy *GIYGTPAGTILYHPHLDIEAFAVDQEVHRIKYGLGLKFAELVYTSFWHSPECKFACHCISKS*EQVEGK

Parental  VQVSVLKGQVYILGRESPLSLYNEELVSMNVQGDYEPIDATGFININSLRLKEYHRLQSKVTAK
          VQ.S...GQVYIL..ESP.SLYN..LVSMN.QGDYEPI.AT..INI.SLRLK.Y.RLQSKVTAK
Retrocopy VQLSIFRGQVYILCQESPQSLYNGKLVSMNMQGDYEPISATSLINIGSLRLKKY-RLQSKVTAK

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	0.29 RPM	51.56 RPM
SRP051959_heart	0.60 RPM	15.54 RPM
SRP051959_kidney	0.62 RPM	351.05 RPM
SRP051959_liver	0.32 RPM	707.59 RPM
SRP051959_lung	0.88 RPM	14.62 RPM
SRP051959_lymph_node	0.66 RPM	4.82 RPM
SRP051959_skeletal_muscle	0.48 RPM	2.01 RPM
SRP051959_spleen	0.82 RPM	10.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1219 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1219 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1219 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2247
Pan troglodytes	retro_ptro_1590
Gorilla gorilla	retro_ggor_1675
Pongo abelii	retro_pabe_1963

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020554	3 retrocopies	retro_cjac_1219 , retro_cjac_4038, retro_cjac_4209,
Homo sapiens	ENSG00000130707	14 retrocopies	retro_hsap_2247, retro_hsap_2885, retro_hsap_3109, retro_hsap_3175, retro_hsap_3252, retro_hsap_3564, retro_hsap_3824, retro_hsap_4149, retro_hsap_4182, retro_hsap_4648, retro_hsap_4743, retro_hsap_4934, retro_hsap_820, retro_hsap_985,
Gorilla gorilla	ENSGGOG00000010228	8 retrocopies	retro_ggor_1346, retro_ggor_1675, retro_ggor_2134, retro_ggor_2403, retro_ggor_2574, retro_ggor_2787, retro_ggor_671, retro_ggor_787,
Myotis lucifugus	ENSMLUG00000006066	2 retrocopies	retro_mluc_1058, retro_mluc_1304,
Mus musculus	ENSMUSG00000076441	1 retrocopy	retro_mmus_135,
Nomascus leucogenys	ENSNLEG00000012500	13 retrocopies	retro_nleu_1088, retro_nleu_1245, retro_nleu_1317, retro_nleu_1381, retro_nleu_1390, retro_nleu_1424, retro_nleu_1701, retro_nleu_1792, retro_nleu_220, retro_nleu_253, retro_nleu_2680, retro_nleu_2764, retro_nleu_625,
Pongo abelii	ENSPPYG00000019692	13 retrocopies	retro_pabe_1963, retro_pabe_2390, retro_pabe_2637, retro_pabe_2696, retro_pabe_2937, retro_pabe_3069, retro_pabe_3197, retro_pabe_3422, retro_pabe_3460, retro_pabe_3521, retro_pabe_3522, retro_pabe_731, retro_pabe_834,
Pan troglodytes	ENSPTRG00000021473	14 retrocopies	retro_ptro_1590, retro_ptro_1951, retro_ptro_2101, retro_ptro_2199, retro_ptro_2268, retro_ptro_2421, retro_ptro_2602, retro_ptro_2821, retro_ptro_2836, retro_ptro_3064, retro_ptro_3158, retro_ptro_3298, retro_ptro_571, retro_ptro_762,