RetrogeneDB ID: retro_cjac_921

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:69612530..69613754(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000016105
• Aliases: None
• Description: None

Sequence

>retro_cjac_921
ATGTAGGAGCCCGGAGCTACTCCTCAGCCCTAGTTGGGGCTGGTCATGGAGAAGCTACACAGGATTGTGGCAGCACTGCC
GGAAAGCATGGTATCAAATTCTAATGGCTTTCCATGGGAATTAGTGATATGGACAGGTGTTATTGGATTTTTTGCTATTC
CCCTTTTTTTGTGGAGAAGTTTTAGATCAGTTAGGAGTTGGCTATATGTGAGAAGAGAGAAAAAGCTTGCTGTAGTGCTT
TGTGAGCAAATTAAAGAAAAATGTAAACTACTTGAAAAATTGAGTTTTCTACAAAAAAGCTATGAAGGCTATGAAGGAGA
GTCATCTTTACAGGACGTCAGCTTCAAGAAGGAGGCAGCAGAAGCACAAAGTTTGGAGGCAAACTGTGAAAAGCTGAGCA
GGTCCATTTCTGAAATGGAGGATGAAATACTGTATGTAAAAAAATAGTTAAAAGAGAAATACAGATATTCTAGACAACAT
CAGTTGATGGCGGATATTTTAGAAATTAGACAGTCTCTAGAAGATCTGGCAAAATCCCTCAAATCACAACTAGCTGAAGC
CAAAATGCCCTTCAATATATTTCAAATGAATGGAGAACAACTGAAGATAGCATTAAAACATGTTTTGAATGAAAATTCTC
AACTTCAGGAAAGCCAGAAACATCTTTTGCAAGAAGCTGAAGTATGGAAAGAACAAGTGAGTGAACTTAATAAACAGAAA
ATAATATTTGAGGATTCCAAAGTCACACAGAACAAGTTCTAAATGACAAAGACAATCACGTTAAGACGCTGACTAAACAC
TTGCTGAAGATGAAAGATTGGGCTGCTATGCTTGGAGAAGACATAATGGATGATCATAACTCAAAAGTAGAAATGAAGAG
TGAATCAGAAAATGGTGCTTCCTTAGCTGATCCTCCAAAAGGAGCTTTGAAGAAACTGATTCATGCTGCTAAGTTAAATG
CTTCTTTAAAAATTTTAGAAGGGGAAAGAAACCAAATTTACATTTAGTTGTCCAAAATTGAGAAAACAGAGAAGCAGCTT
ATGGGGCATATTAAACATCTTCAGTCTGAACAAGCATCTTGGCAGTCAGAAAACAGATTTTGAAAGTGAGAATCAGAAGC
TTCAACAGAAACTTGAAGTAATGACTGAATTACATGAAGAAACAACAGTGAGATTTTAAAAAACATTAACTATAGAGGAA
AATTACCAGTTAGAGAGACGAGAA

Alignment

ORF - retro_cjac_921 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.43 %
• Parental protein coverage: 54.14 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEEPGATPQPYLGLVLEELRRVVAALPEGMRPDSNPYGFPWELVICAAVVGFCAVLFFLWRSFRSVRSRL
          M.EPGATPQP.LGLV.E.L.R.VAALPE.M...SN..GFPWELVI...V.GF.A...FLWRSFRSVRS.L
Retrocopy M*EPGATPQP*LGLVMEKLHRIVAALPESMVSNSN--GFPWELVIWTGVIGFFAIPLFLWRSFRSVRSWL

Parental  YVGREKKLAVMLSGLIEEKCKLLEKFSLVQKEYEGYEVESSLKDASFEKEATEAQSLEATCEKLNRSNSE
          YV.REKKLAV.L...I.EKCKLLEK.S..QK.YEGYE.ESSL.D.SF.KEA.EAQSLEA.CEKL.RS.SE
Retrocopy YVRREKKLAVVLCEQIKEKCKLLEKLSFLQKSYEGYEGESSLQDVSFKKEAAEAQSLEANCEKLSRSISE

Parental  LEDEILCLEKELKEEKSKHSEQDELMADISKRIQSLEDESKSIKSQVAEAKMTFKIFQMNEERLRIAIKD
          .EDEIL...K.LKE.K...S.Q..LMADI....QSLED..KS.KSQ.AEAKM.F.IFQMN.E.L.IA.K.
Retrocopy MEDEILYVKK*LKE-KYRYSRQHQLMADILEIRQSLEDLAKSLKSQLAEAKMPFNIFQMNGEQLKIALKH

Parental  ALNENSQLQESQKQLLQEAEVWKEQVSELNKQKITFEDSKV-HAEEVLNDKENHIKILTERLIKMKDWAA
          .LNENSQLQESQK.LLQEAEVWKEQVSELNKQKI.FEDSKV.H.E.VLNDK.NH.K.LT..L.KMKDWAA
Retrocopy VLNENSQLQESQKHLLQEAEVWKEQVSELNKQKIIFEDSKV<HTEQVLNDKDNHVKTLTKHLLKMKDWAA

Parental  ILGEEITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLE-GERNQIYIQLSDVDKTKE
          .LGE.I.DD.N...EM.SESENGA.L..PPKGALKKLIHAAKLNASLK.LE.G.............K...
Retrocopy MLGEDIMDDHNSKVEMKSESENGASLADPPKGALKKLIHAAKLNASLKILE>GKETKFTFSCPKLRKQRS

Parental  ELTEHIKNLQTEQASLQSENTHFESENQKLQQKLKVMTELYQENEMKLHRKLTVEENFRLEKEE
          .L...I.N.......L.S..T.FESENQKLQQKL.VMTEL..E........LT.EEN..LE..E
Retrocopy SLWG-ILNIFSLNKHLGSQKTDFESENQKLQQKLEVMTELHEETTVRF*KTLTIEENYQLERRE

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	25.65 RPM
SRP051959_heart	0.07 RPM	22.82 RPM
SRP051959_kidney	0.02 RPM	127.75 RPM
SRP051959_liver	0.00 RPM	139.82 RPM
SRP051959_lung	0.07 RPM	25.96 RPM
SRP051959_lymph_node	0.02 RPM	24.68 RPM
SRP051959_skeletal_muscle	0.07 RPM	20.96 RPM
SRP051959_spleen	0.02 RPM	23.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_921 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_921 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_921 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016105	4 retrocopies	retro_cjac_1747, retro_cjac_2711, retro_cjac_3217, retro_cjac_921 ,
Cavia porcellus	ENSCPOG00000026514	2 retrocopies	retro_cpor_189, retro_cpor_727,
Homo sapiens	ENSG00000150527	3 retrocopies	retro_hsap_1201, retro_hsap_3691, retro_hsap_640,
Homo sapiens	ENSG00000258941	1 retrocopy	retro_hsap_78,
Gorilla gorilla	ENSGGOG00000011990	1 retrocopy	retro_ggor_936,
Nomascus leucogenys	ENSNLEG00000004121	10 retrocopies	retro_nleu_1218, retro_nleu_1690, retro_nleu_2087, retro_nleu_2103, retro_nleu_2148, retro_nleu_2600, retro_nleu_2951, retro_nleu_3017, retro_nleu_3077, retro_nleu_688,
Pongo abelii	ENSPPYG00000005768	9 retrocopies	retro_pabe_1001, retro_pabe_1002, retro_pabe_1007, retro_pabe_1055, retro_pabe_1060, retro_pabe_1588, retro_pabe_2119, retro_pabe_29, retro_pabe_3024,
Pan troglodytes	ENSPTRG00000006297	10 retrocopies	retro_ptro_1286, retro_ptro_1712, retro_ptro_2503, retro_ptro_2580, retro_ptro_2880, retro_ptro_466, retro_ptro_821, retro_ptro_826, retro_ptro_868, retro_ptro_876,
Ictidomys tridecemlineatus	ENSSTOG00000015890	1 retrocopy	retro_itri_95,