RetrogeneDB ID: retro_cjac_1251

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:10818826..10819618(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021708
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: B4GALT6
• Ensembl ID: ENSCJAG00000020816
• Aliases: None
• Description: None

Sequence

>retro_cjac_1251
GGATTCCTCAATGTCAATGTAAGTGAAATAAGTTTTGATGAAATTCATCAGCTCTTCTCCAAGGATTTAGACATCGACCA
AGGGGGTCATTGGAGGCCAAAAGACTGTAAACCCGGATGGAAGGTGGCAGTTCTCATTCCTTTCCGTAATCGCCATGAAC
ATTTCCAATTTTTTTCTTACGTCTGATTCCATTGCTCCAGAAGCAAAGACTGGAATTTGTCTTTTATGTCATTGAACAGA
CTGGCACACAACCTTTTAATGCGATGCTCTTCAATGTGGCTTCAAAGAGGCCATGAAAGACAGTATTTGGGACTGTGTAA
TCTTCCACGATGTGGATCATCTACCTGAAAATGACCGGAACTATTACGGATGTGGAGAAATGCCACGTCCTTTTGCTGCA
AAGCTGGATAAATACATGTATATTCTTCCATATAAAGAGTTTTTTGGTGGTGTAAGTGGGCTGACAGTGTTACAATTTAG
AAAGATCAATGGTTTTCCTAATGCCTTCTGGGGATGGGGAGGAGAAGATGATGACCTTTGGAACAGAGTTCACTATGCAG
GATATAATGTAACCAGACCAGGGGAGACTTAGGAAAATACAAGTCAATTCCTTATCACCATAGAGGTGAAGTCCAGTTTT
TAGGACGGTGTAAACTACTAAGGTATTCCAAGGAGCATCAGTACATCGATGGGTTGAACAATTTAATATATAGGCCAAAA
ATACTGGTTGATTGGTTGTATACAAACATATCTGTAAACCTCATGCCAGAGTTAGCTCCAATCAAAGACTAT

Alignment

ORF - retro_cjac_1251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.57 %
• Parental protein coverage: 77.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GFLNVNVSEVSFDEIHQLFSKDLDIEPGGHWRPKDCKPRWKVAVLIPFRNRHEHL-PIFFLHLIPMLQKQ
          GFLNVNVSE.SFDEIHQLFSKDLDI..GGHWRPKDCKP.WKVAVLIPFRNRHEH..PIFFL.LIP.LQKQ
Retrocopy GFLNVNVSEISFDEIHQLFSKDLDIDQGGHWRPKDCKPGWKVAVLIPFRNRHEHF<PIFFLRLIPLLQKQ

Parental  RLEFAFYVIEQTGTQPFNRAMLFNV-GFKEAMKDSIWDCVIFHDVDHLPENDRNYYGCGEMPRHFAAKLD
          RLEF.FYVIEQTGTQPFN.AMLFNV.GFKEAMKDSIWDCVIFHDVDHLPENDRNYYGCGEMPR.FAAKLD
Retrocopy RLEFVFYVIEQTGTQPFN-AMLFNV<GFKEAMKDSIWDCVIFHDVDHLPENDRNYYGCGEMPRPFAAKLD

Parental  KYMYILPYKEFFGGVSGLTVEQFRKINGFPNAFWGWGGEDDDLWNRVHYAGYNVTRP-EGDLGKYKSIPH
          KYMYILPYKEFFGGVSGLTV.QFRKINGFPNAFWGWGGEDDDLWNRVHYAGYNVTRP..GDLGKYKSIP.
Retrocopy KYMYILPYKEFFGGVSGLTVLQFRKINGFPNAFWGWGGEDDDLWNRVHYAGYNVTRP<RGDLGKYKSIPY

Parental  HHRGEVQFLGRYKLLRYSKERQYIDGLNNLIYRPKILVDRLYTNISVNLMPELAPIEDY
          HHRGEVQFLGR.KLLRYSKE.QYIDGLNNLIYRPKILVD.LYTNISVNLMPELAPI.DY
Retrocopy HHRGEVQFLGRCKLLRYSKEHQYIDGLNNLIYRPKILVDWLYTNISVNLMPELAPIKDY

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	0.95 RPM	4.37 RPM
SRP051959_heart	0.46 RPM	4.95 RPM
SRP051959_kidney	0.73 RPM	3.88 RPM
SRP051959_liver	0.58 RPM	16.92 RPM
SRP051959_lung	1.61 RPM	6.83 RPM
SRP051959_lymph_node	2.28 RPM	13.52 RPM
SRP051959_skeletal_muscle	0.61 RPM	0.46 RPM
SRP051959_spleen	1.51 RPM	3.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1251 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1251 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1251 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020816	1 retrocopy	retro_cjac_1251 ,
Ictidomys tridecemlineatus	ENSSTOG00000010911	1 retrocopy	retro_itri_1391,
Tetraodon nigroviridis	ENSTNIG00000010472	1 retrocopy	retro_tnig_6,
Takifugu rubripes	ENSTRUG00000005726	1 retrocopy	retro_trub_9,