RetrogeneDB ID: retro_cjac_1591

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:26074130..26075026(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNL3L
• Ensembl ID: ENSCJAG00000000252
• Aliases: None
• Description: None

Sequence

>retro_cjac_1591
GGAGCCGTTTCTGGGATTACCAAACTCATGCAGGAGGTCCACCTGGACAAGTTAATCTGGCTGCTGGATGCTCCAGGCAT
TGTCCCAGGGCCCGACTCAGAGGTCGGCACCATCCTGCCTAGCTGTGTTCACATGCAGAAGCTGGCAGACCCTGTGACCC
TGGTGGAAACCATCTTGCAATGCTGCAACCTGGAGGAGATTTCCAACAACTACGGGGTCTCTGGGTCCAGACCACTGAGC
AGTTTTGCATGATAGTGGCCCACCATTTGGGGAAGAAGAAGGGAGGCTTATACAGTCAGGAACAGGTGGCCAAAGCTGTT
CTAGCTGACTGGGTCAGTGGGAAGATCAGCTTCTATATATCACCACCACCTACTCACAGTCTGCCCTCCCATCTCAGTGC
TGAGATTGTTAAGGAAGTGACTGAGGTCTTTGACATCGAGGATACTGAGTAGGCCAATGAAACCATGGAATGCTTGGCCA
CTGGAGAATCTGATGAGCTGTTGGGTGCTATGGACCCACTTGAAATGGAGATCAAGTTGCTTCATTCTTCGATGATGAAA
ATAGCAGATGCCATTGAAAGTAAAACCACCATGTATAAGATTGGAGATCTCACTGGGTATTGCACCAATCTGAGCCATCA
TCAGATGGGGTGGGCTAAACACAATGTGAACCACTACCCTAAGAACAACATTATGGTGGATGTCTGCTCAGTGAACTGCT
GCTCAGTGCTGCAGAGGATCATGGAGACAAATCTCCTGCAACAGGGTCAGGCTCTGGCATCTGCCCTGAAGAATAAGATG
ATGCAGAAACGTGCAGACAAAATCGCCAGCAAGCTGTCTGATTCCATGATGTCTGCTCTCGACCTCTCTGGCGGTGCTTA
TGATGGTGTTGGTGAC

Alignment

ORF - retro_cjac_1591 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.17 %
• Parental protein coverage: 51.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAVPGITKFMQEVHLDKFIRLLDAPGIVPGPNSEVGTILRNCVHVQKLADPVTPVETILQRCNLEEISNY
          GAV.GITK.MQEVHLDK.I.LLDAPGIVPGP.SEVGTIL..CVH.QKLADPVT.VETILQ.CNLEEISN.
Retrocopy GAVSGITKLMQEVHLDKLIWLLDAPGIVPGPDSEVGTILPSCVHMQKLADPVTLVETILQCCNLEEISNN

Parental  YGISG-FQTTEHFLTAVAHRLGKKKKGGLYSQEQAAKAVLADWVSGKISFYISPPPTHTLPAHLSAEIVK
          YG.SG..QTTE.F...VAH.LGKKK.GGLYSQEQ.AKAVLADWVSGKISFYISPPPTH.LP.HLSAEIVK
Retrocopy YGVSG<VQTTEQFCMIVAHHLGKKK-GGLYSQEQVAKAVLADWVSGKISFYISPPPTHSLPSHLSAEIVK

Parental  EMTEVFDIEDTEQANEDTMECLATGESDELLGDTDPREMEIKLLHSPMMKIADAIENKTTVYKIGDLTGY
          E.TEVFDIEDTE.ANE.TMECLATGESDELLG..DP.EMEIKLLHS.MMKIADAIE.KTT.YKIGDLTGY
Retrocopy EVTEVFDIEDTE*ANE-TMECLATGESDELLGAMDPLEMEIKLLHSSMMKIADAIESKTTMYKIGDLTGY

Parental  CTNPNRHQMGWAKRNVNHHPKNNNMVDVCSVDRRPVLQRIMETDPLQQGQALASALKNKKKMQKRADKIA
          CTN...HQMGWAK.NVNH.PKNN.MVDVCSV....VLQRIMET..LQQGQALASALKN.K.MQKRADKIA
Retrocopy CTNLSHHQMGWAKHNVNHYPKNNIMVDVCSVNCCSVLQRIMETNLLQQGQALASALKN-KMMQKRADKIA

Parental  SKLSDSMMSALDLSASGDDSVGD
          SKLSDSMMSALDLS....D.VGD
Retrocopy SKLSDSMMSALDLSGGAYDGVGD

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	17.02 RPM
SRP051959_heart	0.00 RPM	23.05 RPM
SRP051959_kidney	0.02 RPM	25.96 RPM
SRP051959_liver	0.04 RPM	19.10 RPM
SRP051959_lung	0.03 RPM	23.13 RPM
SRP051959_lymph_node	0.07 RPM	28.86 RPM
SRP051959_skeletal_muscle	0.00 RPM	34.18 RPM
SRP051959_spleen	0.13 RPM	32.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1591 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1591 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1591 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000252	2 retrocopies	retro_cjac_1591 , retro_cjac_1853,
Homo sapiens	ENSG00000130119	1 retrocopy	retro_hsap_3327,
Gorilla gorilla	ENSGGOG00000007550	1 retrocopy	retro_ggor_1296,
Microcebus murinus	ENSMICG00000010144	1 retrocopy	retro_mmur_662,
Macaca mulatta	ENSMMUG00000008231	1 retrocopy	retro_mmul_2084,
Nomascus leucogenys	ENSNLEG00000016233	1 retrocopy	retro_nleu_1672,
Oryzias latipes	ENSORLG00000014117	1 retrocopy	retro_olat_29,
Pongo abelii	ENSPPYG00000020383	1 retrocopy	retro_pabe_2742,