RetrogeneDB ID: retro_cjac_4067

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:54229725..54231168(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000007299
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBQLN1
• Ensembl ID: ENSCJAG00000003609
• Aliases: None
• Description: None

Sequence

>retro_cjac_4067
ATGGCTGAGAATGGCGAGAGCAGCGGCCCCCCACGCCCCTCCCGCGGCCCTGCTGCGGCCCAAGGCTCGGCTGCTGCCCC
GGCGGAGCCTAAAATCATCAAAGTCACTGTGAAGACTCCCAAAGAGAAAGAGGAGTTCGCGGTGCCCGAGAATAGCTCGG
TCCAGCAGTTTAAGGAAGCGATTTCGAAACGCTTCAAATCCCAAACCGATCAGCTAGTGCTGATTTTTGCCGGAAAAATC
TTAAAAGATCAAGATACCTTGATCCAGCACGGCATCCATGATGGGCTGACTGTTCACCTTGTCATCAAGAGTCAGAACCG
ACCTCAGGGCCAGACCACGCAGCCTAGCAATGCCGCGGGAACTAACACTACCTCGGCGTCGACTCCCAGGAGTAACTCCA
CACCTATTTCCACAAATAGCAACCCGTTTGGGTTGGGGAGCCTGGGAGGACTGGCAGGCCTTAGCAGCCTGGGCTTGAGC
TCGACCAACTTCTCTGAGCTCCAGAGCCAGATGCAGCAGCAACTCATGGCCAGCCCTGAGATGATGATCCAAATCATGGA
AAATCCCTTTGTTCAGAGCATGCTTTCGAATCCCGATCTGATGAGGCAGCTCATTATGGCTAATCCACAGATGCAGCAAT
TGATTCAGAGAAACCCAGAAATCAGTCACCTGCTCAACAACCCAGATATAATGAGGCAGACACTCGAAATTGCCAGGAAT
CCAGCCATGATGCAAGAGATGATGAGAAATCAAGACCTGGCTCTTAGCAATCTCGAAAGCATCCCAGGTGGCTATAATGC
TTTACGGCGCATGTACACTGACATTCAAGAGCCGATGCTGAATGCTGCACAAGAGCAGTTTGGGGGTAATCCGTTTGCCT
CTGTGGGGAGTAGTTCCTCCTCTGGAGAAGGTACGCAGCCTTCCCGCACAGAAAATCGTGATCCACTACCCAATCCATGG
GCACCACCGCCAGCTACCCAGAGTTCTGCAACTACCAGCACGACCACGAGCACTGGTAGTGGGTCTGGCAATAGTTCCAG
CAATGCTACTGGGAACACCGTTGCTGCAGCTAATTATGTCGCCAGTATCTTTAGTACCCCAGGCATGCAGAGCCTGCTGC
AACAGATAACTGAAAACCCCCAGCTGATTCAGAATATGCTGTCGGCGCCCTACATGAGAAGCATGATGCAGTCGCTGAGC
CAGAATCCAGATTTGGCTGCACAGATGATGCTGAATAGCCCGCTGTTTACTGCAAATCCTCAGCTGCAGGAGCAGATGCG
TCCACAGCTCCCAGCCTTCCTGCAGCAGATGCAGAATCCAGATACACTATCTGCCATGTCAAACCCTAGAGCAATGCAGG
CTTTAATGCAGATCCAGCAGGGGCTACAGACATTAGCCACTGAAGCACCTGGCCTCATTCCAAGCTTCACTCCAGGTGTG
GGG

Alignment

ORF - retro_cjac_4067 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.55 %
• Parental protein coverage: 83.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAESGESGGPPGSQDSAAGAEGAGASAAAASAEPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFK
          MAE.GES.GPP......A.A.G.....AAA.AEPKI.KVTVKTPKEKEEFAVPENSSVQQFKE.ISKRFK
Retrocopy MAENGESSGPPRPSRGPAAAQGS----AAAPAEPKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFK

Parental  SHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNRPQDHSAQQTNTTGSNVTTSSAPNSNSTSG
          S.TDQLVLIFAGKILKDQDTL.QHGIHDGLTVHLVIK.QNRPQ....Q..N..G.N.T..S.P.SNST..
Retrocopy SQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKSQNRPQGQTTQPSNAAGTNTTSASTPRSNSTPI

Parental  SATSNPFALGGLGGLAGLSSLGLNTTNFSELQSQMQRQLLSNPEMMVQIMENPFVQSMLSNPDLMRQLIM
          S..SNPF.LG.LGGLAGLSSLGL..TNFSELQSQMQ.QL...PEMM.QIMENPFVQSMLSNPDLMRQLIM
Retrocopy STNSNPFGLGSLGGLAGLSSLGLSSTNFSELQSQMQQQLMASPEMMIQIMENPFVQSMLSNPDLMRQLIM

Parental  ANPQMQQLIQRNPEISHMLNNPDIMRQTLELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTDIQ
          ANPQMQQLIQRNPEISH.LNNPDIMRQTLE.ARNPAMMQEMMRNQD.ALSNLESIPGGYNALRRMYTDIQ
Retrocopy ANPQMQQLIQRNPEISHLLNNPDIMRQTLEIARNPAMMQEMMRNQDLALSNLESIPGGYNALRRMYTDIQ

Parental  EPMLSAAQEQFGGNPFASLVSNTSSGEGSQPSRTENRDPLPNPWAPQTSQSSSASSGTVSTVGGTTGSAA
          EPML.AAQEQFGGNPFAS..S..SSGEG.QPSRTENRDPLPNPWAP.....SSA...T....G...G...
Retrocopy EPMLNAAQEQFGGNPFASVGSSSSSGEGTQPSRTENRDPLPNPWAPPPATQSSATTSTTTSTGSGSGNSS

Parental  SGTAGQSTTMPNLVPGVGASMFNTPGMQSLLQQITENPQLMQNMLSAPYMRSMMQSLSQNPDLAAQMMLN
          S...G......N.V....AS.F.TPGMQSLLQQITENPQL.QNMLSAPYMRSMMQSLSQNPDLAAQMMLN
Retrocopy SNATGNTVAAANYV----ASIFSTPGMQSLLQQITENPQLIQNMLSAPYMRSMMQSLSQNPDLAAQMMLN

Parental  NPLFAGNPQLQEQMRQQLPTFLQQMQNPDTLSAMSNPRAMQALLQIQQGLQTLATEAPGLIPGFTPGLG
          .PLF..NPQLQEQMR.QLP.FLQQMQNPDTLSAMSNPRAMQAL.QIQQGLQTLATEAPGLIP.FTPG.G
Retrocopy SPLFTANPQLQEQMRPQLPAFLQQMQNPDTLSAMSNPRAMQALMQIQQGLQTLATEAPGLIPSFTPGVG

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	2.33 RPM	51.85 RPM
SRP051959_heart	3.60 RPM	40.76 RPM
SRP051959_kidney	3.17 RPM	56.02 RPM
SRP051959_liver	5.50 RPM	58.94 RPM
SRP051959_lung	3.37 RPM	49.50 RPM
SRP051959_lymph_node	3.61 RPM	49.02 RPM
SRP051959_skeletal_muscle	4.28 RPM	50.60 RPM
SRP051959_spleen	3.11 RPM	49.62 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4067 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4067 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4067 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014827	2 retrocopies	retro_btau_1087, retro_btau_188,
Canis familiaris	ENSCAFG00000001435	1 retrocopy	retro_cfam_236,
Callithrix jacchus	ENSCJAG00000003609	2 retrocopies	retro_cjac_3977, retro_cjac_4067 ,
Cavia porcellus	ENSCPOG00000004849	1 retrocopy	retro_cpor_113,
Dasypus novemcinctus	ENSDNOG00000012687	1 retrocopy	retro_dnov_14,
Dipodomys ordii	ENSDORG00000015266	1 retrocopy	retro_dord_680,
Equus caballus	ENSECAG00000019110	1 retrocopy	retro_ecab_1063,
Echinops telfairi	ENSETEG00000002822	1 retrocopy	retro_etel_39,
Felis catus	ENSFCAG00000015049	1 retrocopy	retro_fcat_83,
Homo sapiens	ENSG00000135018	1 retrocopy	retro_hsap_58,
Myotis lucifugus	ENSMLUG00000002036	2 retrocopies	retro_mluc_1774, retro_mluc_33,
Mustela putorius furo	ENSMPUG00000002028	1 retrocopy	retro_mputfur_55,
Mus musculus	ENSMUSG00000005312	1 retrocopy	retro_mmus_83,
Nomascus leucogenys	ENSNLEG00000003306	1 retrocopy	retro_nleu_31,
Otolemur garnettii	ENSOGAG00000012947	1 retrocopy	retro_ogar_276,
Pongo abelii	ENSPPYG00000019323	1 retrocopy	retro_pabe_87,
Pan troglodytes	ENSPTRG00000021055	1 retrocopy	retro_ptro_93,
Rattus norvegicus	ENSRNOG00000019282	1 retrocopy	retro_rnor_339,
Ictidomys tridecemlineatus	ENSSTOG00000013462	1 retrocopy	retro_itri_157,
Tursiops truncatus	ENSTTRG00000004696	1 retrocopy	retro_ttru_1475,