RetrogeneDB ID: retro_cjac_1554

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:44635747..44637424(+)
• Located in intron of: ENSCJAG00000003118

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_1554
ATGAGAAAATTTGCATACTGCAAGGTGGTCCTAACCACCTCCTTGATTTGCGTACTCTTGGATATGTTTCTGCTGCTTTA
CTTCAGTGAATGCAACAAATGTGATGAAAAAAAGGAGAGAGGACTTCCTGCTGGGGATGGTCTAGAGCCAGTACAAAAGC
CTCATGAAGGTCCTGGAGAAATGGGGAAACCAGTCGTCATTCCTAAAGAGGATCAAGAAAAGATGAAAGAGATATTTAAA
ATCAATCAGTTCAATTTAATGGCAAGTGAGATGATTGCACTCAATAGATCTTTACCAGATGTTAGGTTAGAAGGGTGTAA
AACAAAGGTATAGCCAGATAATCTTCCTACAACAGGTGTGGTGATTGTTTTCCACAATGAGGCTTGGAGCACACTTCTGC
AAACTGTCCATAGTGTCATTAATTGCTCACCAAGACACATGATAGAAGAAATTGTTCTAGTAGGTGATGCCAGTGAAAGA
GACTTTTTGAAAAGGTCTTCAGAGAGTTATGTGAAAAAACTGAAAGTACCAGTTCATGTAATTCAAATGGAACAATGTTC
TGGATTGACCAGAACTAGATTAAAAGGAGCTGCAGTTTCTAAAGGCCAAGTGATCACCTTCCTGGGTGCTCATTGTGAGC
GTACAATGGGATGGCTGGAACCTCTCTTGGCCAGGATCAAACATGACAGGAAAACAATGGGTGTCCTATCATCGATGTGA
TCAGTGATGATACTTTTGAGTACATGGCAGGCTCTGATATAACCTATGGCGGGTTCAACTGGAAGCTCAATTTTTGCTGG
TATCCTGTTACCCAAAGAGAAATGGACAGAAGGAAAGGTGATCAGACTCTTCCTGTCAGAACACCTACCATGGCAGGAGG
CCTTTTTTTCAATAGACAGAGATTACTTTCAGGAAATTGGAACATATGATGCTAGAATGGATATTTGGGGAGGAGAAAAC
CTAGAAATTTCCTTTAGGATTTGGCAGTGTGGAGGAACTTTGGAAATTGCTACATGCTCACATGTTGGACATGTGTTTCG
GAAAGCTACACCTTACACGTTTCCAGGAGGTACAGGGCAGATTATCAATAAAAATAACAGACGACTTGCAGAAGTGTGGA
TGGATGAATTCAAGAATTTCTTCTATATAATTTCTCCAGGTGTTGCAAAGGTAGATTATGGAGATATATCATCAAGAGTT
GGTCTAAGACACAAACTACAATGCAAACCTTTTTATTGGTACCTAGAAAATATTTACCCTGATTCTCAAATTCCATGTCA
CTATTTCTCATTGGGAGAGATATGAAACGTGGAAACAAATCAGTGTCTAGATAACATGGCCAGAAAAGAGAAAGAAAAAG
TTGGAATTTTTAATTGCCATGCTATGGGGGGTAATCAGGTTTTCTCTTACATTGCCAACAAAGAAATTAGAACAGATGAC
CTTTGCTTGGATGTCTCCAAACTTAATGGCCCAGTTACAATGCTCAAATGCCACCCCCTAAAAGGCAACCAACTGTGGAA
GTATGACCCAGTGAAATTAACCCTGCAGCATGTGAACAGTAATCAGTACCTAGGTAAAGCCACAGAAGAGGATAGCCAGG
TGCCCAGCATTAGAGACTGCAATGGAAGTCGGTCCCAGCAGTGGCTTCTTTGAAATGTCACCCTGCCAGAAATATTC

Alignment

ORF - retro_cjac_1554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRKFAYCKVVLATSLIWVLLDMFLLLYFSECNKCDEKKERGLPAGDVLEPVQKPHEGPGEMGKPVVIPKE
          MRKFAYCKVVL.TSLI.VLLDMFLLLYFSECNKCDEKKERGLPAGD.LEPVQKPHEGPGEMGKPVVIPKE
Retrocopy MRKFAYCKVVLTTSLICVLLDMFLLLYFSECNKCDEKKERGLPAGDGLEPVQKPHEGPGEMGKPVVIPKE

Parental  DQEKMKEMFKINQFNLMASEMIALNRSLPDVRLEGCKTKVYPDNLPTTSVVIVFHNEAWSTLLRTVHSVI
          DQEKMKE.FKINQFNLMASEMIALNRSLPDVRLEGCKTKV.PDNLPTT.VVIVFHNEAWSTLL.TVHSVI
Retrocopy DQEKMKEIFKINQFNLMASEMIALNRSLPDVRLEGCKTKV*PDNLPTTGVVIVFHNEAWSTLLQTVHSVI

Parental  NRSPRHMIEEIVLVDDASERDFLKRPLESYVKKLKVPVHVIRMEQRSGLIRARLKGAAVSKGQVITFLDA
          N.SPRHMIEEIVLV.DASERDFLKR..ESYVKKLKVPVHVI.MEQ.SGL.R.RLKGAAVSKGQVITFL.A
Retrocopy NCSPRHMIEEIVLVGDASERDFLKRSSESYVKKLKVPVHVIQMEQCSGLTRTRLKGAAVSKGQVITFLGA

Parental  HCECTVGWLEPLLARIKHDRKTV-VCPIIDVISDDTFEYMAGSDMTYGGFNWKLNFRWYPVPQREMDRRK
          HCE.T.GWLEPLLARIKHDRKT...CPIIDVISDDTFEYMAGSD.TYGGFNWKLNF.WYPV.QREMDRRK
Retrocopy HCERTMGWLEPLLARIKHDRKTM<GCPIIDVISDDTFEYMAGSDITYGGFNWKLNFCWYPVTQREMDRRK

Parental  GDRTLPVRTPTMAGGL-FSIDRDYFQEIGTYDAGMDIWGGENLEISFRIWQCGGTLEIVTCSHVGHVFRK
          GD.TLPVRTPTMAGGL.FSIDRDYFQEIGTYDA.MDIWGGENLEISFRIWQCGGTLEI.TCSHVGHVFRK
Retrocopy GDQTLPVRTPTMAGGL>FSIDRDYFQEIGTYDARMDIWGGENLEISFRIWQCGGTLEIATCSHVGHVFRK

Parental  ATPYTFPGGTGQIINKNNRRLAEVWMDEFKNFFYIISPAGVTKVDYGDISSRVGLRHKLQCKPFSWYLEN
          ATPYTFPGGTGQIINKNNRRLAEVWMDEFKNFFYIISP.GV.KVDYGDISSRVGLRHKLQCKPF.WYLEN
Retrocopy ATPYTFPGGTGQIINKNNRRLAEVWMDEFKNFFYIISP-GVAKVDYGDISSRVGLRHKLQCKPFYWYLEN

Parental  IYPDSQIPRHYFSLGEIRNVETNQCLDNMARKENEKVGIFNCHGMGGNQVFSYTANKEIRTDDLCLDVSK
          IYPDSQIP.HYFSLGEI.NVETNQCLDNMARKE.EKVGIFNCH.MGGNQVFSY.ANKEIRTDDLCLDVSK
Retrocopy IYPDSQIPCHYFSLGEI*NVETNQCLDNMARKEKEKVGIFNCHAMGGNQVFSYIANKEIRTDDLCLDVSK

Parental  LNGPVTMLKCHHLKGNQLWEYDPVKLTLQHVNSNQCLDKATEEDSQVPSIRDCNGSRSQQWLLRNVTLPE
          LNGPVTMLKCH.LKGNQLW.YDPVKLTLQHVNSNQ.L.KATEEDSQVPSIRDCNGSRSQQWLL.NVTLPE
Retrocopy LNGPVTMLKCHPLKGNQLWKYDPVKLTLQHVNSNQYLGKATEEDSQVPSIRDCNGSRSQQWLL*NVTLPE

Parental  IF
          IF
Retrocopy IF

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	0.18 RPM	61.30 RPM
SRP051959_heart	0.12 RPM	37.08 RPM
SRP051959_kidney	0.16 RPM	44.57 RPM
SRP051959_liver	0.06 RPM	37.06 RPM
SRP051959_lung	0.15 RPM	54.30 RPM
SRP051959_lymph_node	0.25 RPM	67.94 RPM
SRP051959_skeletal_muscle	0.09 RPM	39.83 RPM
SRP051959_spleen	0.15 RPM	54.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1554 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1554 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1554 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,