RetrogeneDB ID: retro_cjac_446

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:90687157..90688213(+)
• Located in intron of: ENSCJAG00000003268

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000018988
• Aliases: None
• Description: None

Sequence

>retro_cjac_446
AACACTGGGGTCATCAATGCTCCTGAGATGATCATAAAGGAATTTATCAATAGCACTTTGAGGGACAAGGCAAATACCTC
TCCCTCTGAGATGTTGCCCATGTCTCTCTGGTCCTTGTCTGTGGCCATCTCCGTTTGTGGTATGATTGGCTCCTTTTACG
TCGGATTCTTTGTCATCCACTTTGGCAGGTGCAATTCAGTGCTTATCATCAGCCTGTTGGCTGTCACTGGTGGCTGCCTC
ATGGGATCGTGTAAAGTAGCTGAGTTGCTTGAAATGCTCATCCTGGGCCGCTTAGTTATTGACCTCTTCTGCAGACTATG
CACAGGTTTTGTGCCCATGTACATGTGGAGAGATCTCACCTACTGCCCTGCAGGGTGCCTTTGGTACTCTAAACCAGCTG
AACATTGTTGGAATTCTGGTGGCCCAGGTCTTTGGTCTGGAATTTCTGGAATTCATCCTTGGGTCTGAAGAGCTGCGGCC
AGTGCTGTTGGGCTTTACCATCCTTACTGCTATCCTACAAAGTGCAGCCCTTCCATTTTGCCCTGAAAGTCCCAGATTTT
TGCTCATTAACAGAAAAGAAGAGGATGCTTAGTAGATCCTCCAGTGGTTGTCGGGCACCCAAGATGTATCCCAAGACATC
CAGGAGATGAGCGATGAGAATGCAAGAATGCCACAAGAAAAGCAAGTCACCGTGCTGGAGCACTTTAGAGTATCCAGCTG
CCGACAGCCCATCATCATTTCCATTGTGCTCCAGCTCTCTCAGCAGCTCTCTGGAATCAATGCTGTGTTCTGTTACTCAA
CAGGAATCTTCAAGGATGCAGGTGTTCAAGAACCCATCTATGCCACCATCGGTGAAGGTGTGGCTAATACTGTCTTCACT
GTCGTTTTCCTGTTTCTGGTGGAAAGGGCAGGAAGAAGGACTCTGCATATGATAGACCTTGGAGGGATGGCTTTTTGTCC
CATACACACGACTGTTTTTTTTAGTTATTAAAGGATGACTGTAATGGGATGAGCTTTGTCTGTATTAGGGCTATCTTGGT
CTTTATTCCCTGGTTT

Alignment

ORF - retro_cjac_446 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.11 %
• Parental protein coverage: 70.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NTGVINAPEMIIKEFVNNTLKNKKNAPPSEMLLTSLWSLSVAIFSVGGMIGSFSVGLFVNRFGRRNSMLI
          NTGVINAPEMIIKEF.N.TL..K.N..PSEML..SLWSLSVAI.SV.GMIGSF.VG.FV..FGR.NS.LI
Retrocopy NTGVINAPEMIIKEFINSTLRDKANTSPSEMLPMSLWSLSVAI-SVCGMIGSFYVGFFVIHFGRCNSVLI

Parental  VNLLAVTGGCLMGLCKMAESVEMLILGRLVIGLFCGLCTGFVPMYI-GEISPTALRGAFGTLNQLGIVVG
          ..LLAVTGGCLMG.CK.AE..EMLILGRLVI.LFC.LCTGFVPMY..GEISPTAL.GAFGTLNQL.IV.G
Retrocopy ISLLAVTGGCLMGSCKVAELLEMLILGRLVIDLFCRLCTGFVPMYM>GEISPTALQGAFGTLNQLNIV-G

Parental  ILVAQIFG---LEFILGSEVLWPVLLGFTILPAILQSAALPFCPESPRFLLINRKEEENAKQILQRLWGT
          ILVAQ.FG...LEFILGSE.L.PVLLGFTIL.AILQSAALPFCPESPRFLLINRKEE..A..ILQ.L.GT
Retrocopy ILVAQVFGLEFLEFILGSEELRPVLLGFTILTAILQSAALPFCPESPRFLLINRKEED-A**ILQWLSGT

Parental  QDVSQDIQEMKEESARMSQEKQVTVLELFRVSSYRQPIIISIVLQLSQQLSGINAVFYYSTGIFKDAGVQ
          QDVSQDIQEM..E.ARM.QEKQVTVLE.FRVSS.RQPIIISIVLQLSQQLSGINAVF.YSTGIFKDAGVQ
Retrocopy QDVSQDIQEMSDENARMPQEKQVTVLEHFRVSSCRQPIIISIVLQLSQQLSGINAVFCYSTGIFKDAGVQ

Parental  EPIYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMALCSLLMTV-SLLLK-DNYNGMSFVCIGAI
          EPIYATIG.GV.NT.FTVV.LFLVERAGRRTLHMI.LGGMA.C....TV..L..K.D..NGMSFVCI.AI
Retrocopy EPIYATIGEGVANTVFTVVFLFLVERAGRRTLHMIDLGGMAFCPIHTTV>FLVIK>DDCNGMSFVCIRAI

Parental  LVFVAFF
          LVF...F
Retrocopy LVFIPWF

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	2.06 RPM	9.07 RPM
SRP051959_heart	1.70 RPM	8.16 RPM
SRP051959_kidney	1.09 RPM	1.69 RPM
SRP051959_liver	0.50 RPM	0.71 RPM
SRP051959_lung	2.07 RPM	7.81 RPM
SRP051959_lymph_node	0.75 RPM	9.61 RPM
SRP051959_skeletal_muscle	0.61 RPM	2.31 RPM
SRP051959_spleen	1.68 RPM	5.25 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_446 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_446 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_446 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004556	2 retrocopies	retro_btau_708, retro_btau_709,
Callithrix jacchus	ENSCJAG00000018988	1 retrocopy	retro_cjac_446 ,
Cavia porcellus	ENSCPOG00000003074	1 retrocopy	retro_cpor_761,
Cavia porcellus	ENSCPOG00000009834	1 retrocopy	retro_cpor_760,
Cavia porcellus	ENSCPOG00000011295	1 retrocopy	retro_cpor_587,
Felis catus	ENSFCAG00000001625	1 retrocopy	retro_fcat_1924,
Homo sapiens	ENSG00000059804	2 retrocopies	retro_hsap_3983, retro_hsap_401,
Gorilla gorilla	ENSGGOG00000016813	1 retrocopy	retro_ggor_398,
Macaca mulatta	ENSMMUG00000000439	2 retrocopies	retro_mmul_2301, retro_mmul_502,
Nomascus leucogenys	ENSNLEG00000026903	2 retrocopies	retro_nleu_1572, retro_nleu_1904,
Oryctolagus cuniculus	ENSOCUG00000008575	1 retrocopy	retro_ocun_352,
Pongo abelii	ENSPPYG00000004234	1 retrocopy	retro_pabe_3274,
Pongo abelii	ENSPPYG00000004235	1 retrocopy	retro_pabe_315,
Pan troglodytes	ENSPTRG00000004624	1 retrocopy	retro_ptro_2703,
Pan troglodytes	ENSPTRG00000004626	1 retrocopy	retro_ptro_307,