RetrogeneDB ID: retro_cjac_4083

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:68780591..68781413(+)
• Located in intron of: ENSCJAG00000021170

Retrocopy information

• Ensembl ID: ENSCJAG00000033094
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: METTL9
• Ensembl ID: ENSCJAG00000020564
• Aliases: None
• Description: methyltransferase like 9 [Source:HGNC Symbol;Acc:24586]

Sequence

>retro_cjac_4083
GCGGCCCGGGTGGGCCGCCGGAAGGAGAACCACCAGTGTTATGTGTGCAACAGAGAGAAATTATGCGAATCACTCCAGGC
TGTCTTTGTTCAGAGTTACCTTGATCAAGGAACACAGATCTTCTTAAATAACAGCATTGAGAAATCTGGCTGGCTATTTA
TCCAATTATATCATTCTTTTGTGTCATCTGTTTTTAGCCTGTTTATGTCTAGAACATCTATCAATGGATTGCTAGGAAGA
GGCTCAATGTTTGTGTTTTCACCAGATCAGTTTCAGAGACTGCTTAAAATTAATCCAGACTGGAAAACCGACAGACTTCT
TGATTTAGGTGCTGGAGATGGAGAGGTCACAAAAATCATGAGCCCTCATTTTGAAGAAATCTATGCCACTGAGCTTTCTG
AAACTATGATATGGCAGCTTCAGAAGAAAAAATACAGAGTGCTTGGTATAAATGAATGGCAGAATACAGGGTTCCAGTAT
GATGTCATTAGCTGCCTGAACTTGCTGGACCACTGTGATCAGCCCCTGACTTTGTTAAAGAATATCAGAAGTGTCTTGGA
GCCAACTAGAGGCAGGGTCATCCTTGCCCTGGTCCTTCCCTTTCATCCCTATGTGGAAAATGGTGGCAAGTGGGAGAAAC
CATCAGAAATTTTGGAAATCAAGGGACAGAACTGGGAAGAACAAGTGAATAGTCTGCCTGAAGTTTTCAGAAAAGCCAGT
TTTGTTATTGAAGCTTTCACCAGACTACCATACCTGTGTGAAGGTTACATGTATAATGACTACTACATTCTGGATGATGC
TGTCTTTGTTCTCAAACCAGTA

Alignment

ORF - retro_cjac_4083 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.64 %
• Parental protein coverage: 86.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAAGGGKENHQWYVCNREKLCESLQAVFVQSYLDQGTQIFLNNSIEKSGWLFIQLYHSFVSSVFSLFMS
          AA..G..KENHQ.YVCNREKLCESLQAVFVQSYLDQGTQIFLNNSIEKSGWLFIQLYHSFVSSVFSLFMS
Retrocopy AARVGRRKENHQCYVCNREKLCESLQAVFVQSYLDQGTQIFLNNSIEKSGWLFIQLYHSFVSSVFSLFMS

Parental  RTSINGLLGRGSMFVFSPDQFQRLLKINPDWKTHRLLDLGAGDGEVTKIMSPHFEEIYATELSETMIWQL
          RTSINGLLGRGSMFVFSPDQFQRLLKINPDWKT.RLLDLGAGDGEVTKIMSPHFEEIYATELSETMIWQL
Retrocopy RTSINGLLGRGSMFVFSPDQFQRLLKINPDWKTDRLLDLGAGDGEVTKIMSPHFEEIYATELSETMIWQL

Parental  QKKKYRVLGINEWQNTGFQYDVISCLNLLDRCDQPLTLLKDIRSVLEPTRGRVILALVLPFHPYVENVGG
          QKKKYRVLGINEWQNTGFQYDVISCLNLLD.CDQPLTLLK.IRSVLEPTRGRVILALVLPFHPYVEN.GG
Retrocopy QKKKYRVLGINEWQNTGFQYDVISCLNLLDHCDQPLTLLKNIRSVLEPTRGRVILALVLPFHPYVEN-GG

Parental  KWEKPSEILEIKGQNWEEQVNSLPEVFRKAGFVIEAFTRLPYLCEGDMYNDYYVLDDAVFVLKPV
          KWEKPSEILEIKGQNWEEQVNSLPEVFRKA.FVIEAFTRLPYLCEG.MYNDYY.LDDAVFVLKPV
Retrocopy KWEKPSEILEIKGQNWEEQVNSLPEVFRKASFVIEAFTRLPYLCEGYMYNDYYILDDAVFVLKPV

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	0.38 RPM	21.46 RPM
SRP051959_heart	0.51 RPM	14.19 RPM
SRP051959_kidney	0.82 RPM	57.04 RPM
SRP051959_liver	0.22 RPM	6.97 RPM
SRP051959_lung	0.65 RPM	21.51 RPM
SRP051959_lymph_node	1.00 RPM	19.82 RPM
SRP051959_skeletal_muscle	0.22 RPM	13.32 RPM
SRP051959_spleen	0.53 RPM	20.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4083 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4083 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4083 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003533	2 retrocopies	retro_amel_402, retro_amel_704,
Canis familiaris	ENSCAFG00000017710	1 retrocopy	retro_cfam_1875,
Callithrix jacchus	ENSCJAG00000020564	1 retrocopy	retro_cjac_4083 ,
Mustela putorius furo	ENSMPUG00000016801	2 retrocopies	retro_mputfur_1323, retro_mputfur_1610,
Oryctolagus cuniculus	ENSOCUG00000004285	1 retrocopy	retro_ocun_754,
Otolemur garnettii	ENSOGAG00000008169	3 retrocopies	retro_ogar_1745, retro_ogar_307, retro_ogar_588,
Rattus norvegicus	ENSRNOG00000025940	1 retrocopy	retro_rnor_2623,
Sus scrofa	ENSSSCG00000030373	1 retrocopy	retro_sscr_441,
Tupaia belangeri	ENSTBEG00000003816	2 retrocopies	retro_tbel_1726, retro_tbel_2084,
Tursiops truncatus	ENSTTRG00000015624	4 retrocopies	retro_ttru_1100, retro_ttru_1466, retro_ttru_163, retro_ttru_467,