RetrogeneDB ID: retro_cjac_865

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:83392187..83393531(+)
• Located in intron of: ENSCJAG00000006739

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALNT1
• Ensembl ID: ENSCJAG00000021030
• Aliases: None
• Description: None

Sequence

>retro_cjac_865
ATGAGAAAATTTGCATACTGAAAGATGGTCCTAGCCACCTCCTTGATTTGGGTACTCTTGGATATGTTCCTGCTGCTTTA
CTTCAGTAAATGCAACAAATGTGATGAAAAAAAGGAGAAAGGATTTCCTGCTGGGGATATTCTAGAGCCAGTACAAAAAC
CTCATGAAGGTCCTGGAGAAATGGGAAAACCAGTCATAATCCCTAAAGAGGATCAAGAAAAGTTGAAAGAGATCTTTAAA
ATCATTCAATTCAATTTAATCGCAAGTGAAATGATTGCACTCAACAGATCTTTATCAGATGTTAGGTTAGAAGAGTGTAA
AACAAAGGTATATCCAGGTATTCTTCCTACAAGTGTGGTGATTGTTTTCTGCAATAAGGCTTGGAGCACACTTCTGCCAA
CTGTCTATAGTGTCATTAATTGCTCACCAAGAAACTGGATGGAAGAAATTGTTCTAGTAAATGATGGCAGTGAAAGAGAC
TTTTTGAAAAGGATTTTAGAGAGTTATGTGAAAAAACTAAGAGTACCAGTTCATATAATTCAAATGGAACAACGTTTTGG
ATGGATCAGAGCTAGATTAAAAGGAGCTGCTCTGTCTACAGACCAAGTGATCACCTTCCTGGATGCTCATTGTGAGTGTA
CAGTGGGGTGGCTGAAGCCTTTCTTGGCCAGGATCAAACATGACAGGAGAACAGTGGTGTGTCCTATCATCAATGTGATC
AGCGATGATACTTTTGAGTACATAGCAGGCTCTGATATGACTTATGGTAGGTTCAAGTGGAAGCTCAATTTTTGCTGGTA
TCCTGTTCCCCAGAGAGAAATGGGCAGAAGGAAAGGTGATCGGACACTTCGCATTAGAACACCTACCATGGCAGAAGGCC
TTTTTTCAATAGACAGAGATTACTTTCAGGAAATGGGAACATATGATGCTGAAAAGGATATCTGGGGAGGAGAAAACCTA
GAAATTTCCTTTCAGATTTGACAGTGTGGAGGAACTTTGGAAACTGTTACATGCTCACATGTTAGACATGTGTTTCAAAA
AGCTACAACTTACACATTTCCAGGAGGCACAGGGCAGATTATCAATAAAAATAATAGACAATTTGCAGAAGTGTGGATGG
ATGAATTCAAGAATTTCTTCTATATAATTTCTCCAGATGTTACAACGGCAGATTATGGAGCTATATCATCAAGAGCTGGT
CTAAGACACAAACTACAATGCAAACCTTTTTCTTGGTACTTAGAGAATATTTATCCTGATTCTCAAATTCCATGTCACTA
TTTCTCATTGGGAGAGATGAGAAGTGTGGAAATAAATCAGTGTCTAGATAACATAGCTAGAAAA

Alignment

ORF - retro_cjac_865 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.67 %
• Parental protein coverage: 80.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRKFAYCKVVLATSLIWVLLDMFLLLYFSECNKCDEKKERGLPAGDVLEPVQKPHEGPGEMGKPVVIPKE
          MRKFAY.K.VLATSLIWVLLDMFLLLYFS.CNKCDEKKE.G.PAGD.LEPVQKPHEGPGEMGKPV.IPKE
Retrocopy MRKFAY*KMVLATSLIWVLLDMFLLLYFSKCNKCDEKKEKGFPAGDILEPVQKPHEGPGEMGKPVIIPKE

Parental  DQEKMKEMFKINQFNLMASEMIALNRSLPDVRLEGCKTKVYPDNLPTTSVVIVFHNEAWSTLLRTVHSVI
          DQEK.KE.FKI.QFNL.ASEMIALNRSL.DVRLE.CKTKVYP..LPT.SVVIVF.N.AWSTLL.TV.SVI
Retrocopy DQEKLKEIFKIIQFNLIASEMIALNRSLSDVRLEECKTKVYPGILPT-SVVIVFCNKAWSTLLPTVYSVI

Parental  NRSPRHMIEEIVLVDDASERDFLKRPLESYVKKLKVPVHVIRMEQRSGLIRARLKGAAVSKGQVITFLDA
          N.SPR...EEIVLV.D.SERDFLKR.LESYVKKL.VPVH.I.MEQR.G.IRARLKGAA.S..QVITFLDA
Retrocopy NCSPRNWMEEIVLVNDGSERDFLKRILESYVKKLRVPVHIIQMEQRFGWIRARLKGAALSTDQVITFLDA

Parental  HCECTVGWLEPLLARIKHDRKTVVCPIIDVISDDTFEYMAGSDMTYGGFNWKLNFRWYPVPQREMDRRKG
          HCECTVGWL.P.LARIKHDR.TVVCPII.VISDDTFEY.AGSDMTYG.F.WKLNF.WYPVPQREM.RRKG
Retrocopy HCECTVGWLKPFLARIKHDRRTVVCPIINVISDDTFEYIAGSDMTYGRFKWKLNFCWYPVPQREMGRRKG

Parental  DRTLPVRTPTMAGGLFSIDRDYFQEIGTYDAGMDIWGGENLEISFRIWQCGGTLEIVTCSHVGHVFRKAT
          DRTL..RTPTMA.GLFSIDRDYFQE.GTYDA..DIWGGENLEISF.I.QCGGTLE.VTCSHV.HVF.KAT
Retrocopy DRTLRIRTPTMAEGLFSIDRDYFQEMGTYDAEKDIWGGENLEISFQI*QCGGTLETVTCSHVRHVFQKAT

Parental  PYTFPGGTGQIINKNNRRLAEVWMDEFKNFFYIISPAGVTKVDYGDISSRVGLRHKLQCKPFSWYLENIY
          .YTFPGGTGQIINKNNR..AEVWMDEFKNFFYIISP..VT..DYG.ISSR.GLRHKLQCKPFSWYLENIY
Retrocopy TYTFPGGTGQIINKNNRQFAEVWMDEFKNFFYIISP-DVTTADYGAISSRAGLRHKLQCKPFSWYLENIY

Parental  PDSQIPRHYFSLGEIRNVETNQCLDNMARK
          PDSQIP.HYFSLGE.R.VE.NQCLDN.ARK
Retrocopy PDSQIPCHYFSLGEMRSVEINQCLDNIARK

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	0.02 RPM	61.30 RPM
SRP051959_heart	0.05 RPM	37.08 RPM
SRP051959_kidney	0.00 RPM	44.57 RPM
SRP051959_liver	0.02 RPM	37.06 RPM
SRP051959_lung	0.03 RPM	54.30 RPM
SRP051959_lymph_node	0.00 RPM	67.94 RPM
SRP051959_skeletal_muscle	0.02 RPM	39.83 RPM
SRP051959_spleen	0.02 RPM	54.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_865 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_865 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_865 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011206	1 retrocopy	retro_btau_581,
Callithrix jacchus	ENSCJAG00000021030	2 retrocopies	retro_cjac_1554, retro_cjac_865 ,
Myotis lucifugus	ENSMLUG00000001978	1 retrocopy	retro_mluc_163,
Mus musculus	ENSMUSG00000000420	1 retrocopy	retro_mmus_1312,
Ictidomys tridecemlineatus	ENSSTOG00000003311	1 retrocopy	retro_itri_954,
Tarsius syrichta	ENSTSYG00000014610	1 retrocopy	retro_tsyr_1444,