RetrogeneDB ID: retro_cjac_2888

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:62797994..62798570(+)
• Located in intron of: ENSCJAG00000009742

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL1
• Ensembl ID: ENSCJAG00000006615
• Aliases: None
• Description: methyltransferase like 1 [Source:HGNC Symbol;Acc:7030]

Sequence

>retro_cjac_2888
GGCTGTGGCTATGGTGGCCCATTAGTGGAACTGTCACCGCTGTTCCCAGACACACTGATTCTGGGTCTGGAGATCCGGGT
GAAGGTCTCAGACTATGTTCAAGACCGGATTCGGGTCCTATGCGCAGCTCCCGGAGGTGGCTTCCAGAACATCGCCTGTC
TCCGTAGCAATGCCATGAAGCACCTTCCTAACTTCTACAAGGGCCAGCTGATAAAGATGTTCTTCCTCTTCCCCGACCCA
CATTTCAAGCGGACAAAGCACAAGTGGCGAATCATCAGTCCCACACTGCTAGCAGAATATGCCTATGTGCTGAGAGTTGG
GGGGCTGATGTATACCATAACCGATGTGCTGGAGCTACATGACTGGATGAGCACTCATTTTGAAGAGCACCTGCTGTTTG
AGCGTGTGCCCCTGGAGGACCTGAGTGAAGACCCTATTGTGGGACATCTAGGCATCTCAACTGAGGAGGGGAAGAAAGTT
CTACGTAACGGAGGGAAGAATTTCCCAGCCATCTTCCGAAGAATACAAGATCCCGTCCTCCAGGCAGTAACCCCCCAATC
CAGCCTGCCTGGTCAC

Alignment

ORF - retro_cjac_2888 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.3 %
• Parental protein coverage: 69.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GCGYGGLLVELSPLFPDTLILGLEIRVKVSDYVQDRIRALRAAPGGGFQNIACLRSNAMKHLPNFFYKGQ
          GCGYGG.LVELSPLFPDTLILGLEIRVKVSDYVQDRIR.L.AAPGGGFQNIACLRSNAMKHLPNF.YKGQ
Retrocopy GCGYGGPLVELSPLFPDTLILGLEIRVKVSDYVQDRIRVLCAAPGGGFQNIACLRSNAMKHLPNF-YKGQ

Parental  LTKMFFLFPDPHFKRTKHKWRIISPTLLAEYAYVLRVGGLVYTITDVLELHDWMCTHFEEHPLFERVPLE
          L.KMFFLFPDPHFKRTKHKWRIISPTLLAEYAYVLRVGGL.YTITDVLELHDWM.THFEEH.LFERVPLE
Retrocopy LIKMFFLFPDPHFKRTKHKWRIISPTLLAEYAYVLRVGGLMYTITDVLELHDWMSTHFEEHLLFERVPLE

Parental  DLSEDPIVGHLGTSTEEGKKVLRNGGKNFPAIFRRIQDPILQAVNPQSSLPGH
          DLSEDPIVGHLG.STEEGKKVLRNGGKNFPAIFRRIQDP.LQAV.PQSSLPGH
Retrocopy DLSEDPIVGHLGISTEEGKKVLRNGGKNFPAIFRRIQDPVLQAVTPQSSLPGH

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	0.27 RPM	1.15 RPM
SRP051959_heart	0.11 RPM	0.98 RPM
SRP051959_kidney	0.09 RPM	3.59 RPM
SRP051959_liver	0.09 RPM	1.56 RPM
SRP051959_lung	0.20 RPM	1.15 RPM
SRP051959_lymph_node	0.64 RPM	1.35 RPM
SRP051959_skeletal_muscle	0.22 RPM	2.53 RPM
SRP051959_spleen	0.17 RPM	1.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2888 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2888 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2888 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006615	1 retrocopy	retro_cjac_2888 ,
Homo sapiens	ENSG00000037897	1 retrocopy	retro_hsap_4796,
Gorilla gorilla	ENSGGOG00000001411	1 retrocopy	retro_ggor_2985,
Microcebus murinus	ENSMICG00000003803	1 retrocopy	retro_mmur_345,
Macaca mulatta	ENSMMUG00000022148	1 retrocopy	retro_mmul_2556,
Nomascus leucogenys	ENSNLEG00000017183	1 retrocopy	retro_nleu_1110,
Pongo abelii	ENSPPYG00000004706	1 retrocopy	retro_pabe_3730,
Tupaia belangeri	ENSTBEG00000011522	1 retrocopy	retro_tbel_3245,