RetrogeneDB ID: retro_cjac_196

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:1646728..1647913(+)
• Located in intron of: ENSCJAG00000009788

Retrocopy information

• Ensembl ID: ENSCJAG00000021994
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DDI2
• Ensembl ID: ENSCJAG00000008625
• Aliases: None
• Description: DNA-damage inducible 1 homolog 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:24578]

Sequence

>retro_cjac_196
ATGCTCATCACCGTGTACTGCGTGCGGAGGGACCTCTCGGAAGTCACCTTCTCCCTCCAGGTCAGCCCTGACTTTGAGCT
CCGAAACTTCAAGGTCCTCTGCGAGGTGGAGTCCAGAGTCCCCGCCGACGAGATCCAGATCATCCACATGGAGCGACTCC
TCATTGACGACCACTGTTCCCTGGGCTCCTACGGCCTCAAAGACGGCGATGTGGTGGTTTTACTGCAGAGGGACAACGTG
GGACCCCGGGCCCCGAACCAGCCTCGTGTAGACTTGAGCGGCGGCATCGCAGCACCCGGGACGTCCAGCTCCCGCCCGCA
GCACCCAGGACAGCAGCGGCAGCAGCGCGCACCCTCTGCCCAGCGGGCGCACGGCCGGGCCTTGGGGGAGGAGGCGGCCG
GCCCGCAAGGCCTGGGCAGCCCAGCCCTGATCCGCAGCACGCTGCTCTCCAACCGGCACCATCTGTCCCTGCTCGAGGAA
CGCAACCCCAGCCTGGCGGAGGCCCTGCTCAGCGGAAGCCTTGACACCTTTGCTCAGGTGCTGATGGAGCAGCGAAGGGA
ATGGGCCTCGAGAGAGCGGGAGAGGCTTCGTCTCTACACGGCCGACCCCCTGGATCTGGAAGCTCAGGCCAAAATAGAAG
AGGAGATCCGGCAGAGGAACGTGGAAGAAAACATGAATATAGCGATGGAAGAGGCGCCCGAGACTTTCGGACAAGTGACG
ATGCTCTACATTAACTGCAGAGTGAACGGGCGTCCTTTGAAGGCGTTTGTTGACTCGGGCGCCCAGATGACCATCATGAG
CCAGGCTTGTGCCGAGCGCTGTAACATCATGAGGCTGGTGGACCGACGGTGGGCTGGGGTTGCTCAAGGAGTGGGCACGC
AGATCATTATCGGCCGCGTTCATCTGGCTCAGATTCAAATTGAAGGTGATTTCTTACCGTGCTCTTTCTCCATACTTGCG
GACCAACCCATGGATATGCTTCTAGGCCTAGATATGCTCCGAAGACATCAATGTTCCATCGATTTGAAGAAAAACGTGCT
GGTCATCGGCACCACTGGCACGCAGACCTACTTCCTTCCTGAGGGAGAGTCGCCCTTACTCAGTAGGATGGTAAATGGGC
AAGATGGGCCTTCTGACAAGGAAATTACACATTCGGGCAAGGATTTCGGACAAAAAGAGCACTGA

Alignment

ORF - retro_cjac_196 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.33 %
• Parental protein coverage: 65.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RPRQPPGTQQSHSSP-GEIASSPQGLDNPALLRDMLLANPHELSLLKERNPPLAEALLSGDLEKFSRVLV
          R....P..Q..H....GE.A..PQGL..PAL.R..LL.N.H.LSLL.ERNP.LAEALLSG.L..F..VL.
Retrocopy RQQRAPSAQRAHGRALGEEAAGPQGLGSPALIRSTLLSNRHHLSLLEERNPSLAEALLSGSLDTFAQVLM

Parental  EQQQDRARREQERIRLFSADPFDLEAQAKIEEDIRQQNIEENMTIAMEEAPESFGQVVMLYINCKVNGHP
          EQ....A.RE.ER.RL..ADP.DLEAQAKIEE.IRQ.N.EENM.IAMEEAPE.FGQV.MLYINC.VNG.P
Retrocopy EQRREWASRERERLRLYTADPLDLEAQAKIEEEIRQRNVEENMNIAMEEAPETFGQVTMLYINCRVNGRP

Parental  VKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGIAKGVGTQKIIGRVHLAQVQIEGDFLACSFSILEEQ
          .KAFVDSGAQMTIMSQACAERCNIMRLVDRRWAG.A.GVGTQ.IIGRVHLAQ.QIEGDFL.CSFSIL..Q
Retrocopy LKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAQGVGTQIIIGRVHLAQIQIEGDFLPCSFSILADQ

Parental  PMDMLLGLDMLKRHQCSIDLKKNVLVIGTTGSQTTFLPEGELPECARLAYG
          PMDMLLGLDML.RHQCSIDLKKNVLVIGTTG.QT.FLPEGE.P...R...G
Retrocopy PMDMLLGLDMLRRHQCSIDLKKNVLVIGTTGTQTYFLPEGESPLLSRMVNG

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	0.09 RPM	28.38 RPM
SRP051959_heart	0.14 RPM	17.10 RPM
SRP051959_kidney	0.11 RPM	21.32 RPM
SRP051959_liver	0.04 RPM	20.99 RPM
SRP051959_lung	0.03 RPM	22.82 RPM
SRP051959_lymph_node	0.00 RPM	20.20 RPM
SRP051959_skeletal_muscle	0.07 RPM	29.11 RPM
SRP051959_spleen	0.15 RPM	23.36 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_196 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_196 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_196 has 11 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_96
Pan troglodytes	retro_ptro_570
Gorilla gorilla	retro_ggor_143
Pongo abelii	retro_pabe_158
Macaca mulatta	retro_mmul_231
Mus musculus	retro_mmus_67
Oryctolagus cuniculus	retro_ocun_249
Bos taurus	retro_btau_15
Sus scrofa	retro_sscr_6
Canis familiaris	retro_cfam_193
Equus caballus	retro_ecab_110

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011873	1 retrocopy	retro_amel_10,
Bos taurus	ENSBTAG00000018718	2 retrocopies	retro_btau_15, retro_btau_650,
Canis familiaris	ENSCAFG00000016220	1 retrocopy	retro_cfam_193,
Callithrix jacchus	ENSCJAG00000008625	1 retrocopy	retro_cjac_196 ,
Cavia porcellus	ENSCPOG00000020885	1 retrocopy	retro_cpor_88,
Equus caballus	ENSECAG00000000762	1 retrocopy	retro_ecab_110,
Homo sapiens	ENSG00000197312	1 retrocopy	retro_hsap_96,
Gorilla gorilla	ENSGGOG00000013537	1 retrocopy	retro_ggor_143,
Macropus eugenii	ENSMEUG00000006148	1 retrocopy	retro_meug_1364,
Myotis lucifugus	ENSMLUG00000030669	1 retrocopy	retro_mluc_68,
Macaca mulatta	ENSMMUG00000019912	1 retrocopy	retro_mmul_231,
Monodelphis domestica	ENSMODG00000003515	1 retrocopy	retro_mdom_282,
Mustela putorius furo	ENSMPUG00000016332	1 retrocopy	retro_mputfur_1509,
Mus musculus	ENSMUSG00000078515	1 retrocopy	retro_mmus_67,
Oryctolagus cuniculus	ENSOCUG00000023891	1 retrocopy	retro_ocun_249,
Otolemur garnettii	ENSOGAG00000027709	1 retrocopy	retro_ogar_4,
Ochotona princeps	ENSOPRG00000018448	1 retrocopy	retro_opri_4,
Pongo abelii	ENSPPYG00000001841	1 retrocopy	retro_pabe_158,
Pan troglodytes	ENSPTRG00000024059	1 retrocopy	retro_ptro_570,
Pteropus vampyrus	ENSPVAG00000005084	1 retrocopy	retro_pvam_420,
Rattus norvegicus	ENSRNOG00000012274	1 retrocopy	retro_rnor_2606,
Sus scrofa	ENSSSCG00000003462	1 retrocopy	retro_sscr_6,
Ictidomys tridecemlineatus	ENSSTOG00000019447	1 retrocopy	retro_itri_93,
Tarsius syrichta	ENSTSYG00000002522	1 retrocopy	retro_tsyr_1120,