RetrogeneDB ID: retro_cjac_4184

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:69086476..69087700(-)
• Located in intron of: ENSCJAG00000004052

Retrocopy information

• Ensembl ID: ENSCJAG00000023354
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000016908
• Aliases: None
• Description: None

Sequence

>retro_cjac_4184
ATGCAGGTCACCCTGAAGACCCTCCAGCAGCAGACCTTCAAGATAGACATCGACCCCGAGGAGACGGTGAAAGCACTGAA
AGAGAAGACTGAATCTGAAAAGGGGAAAGATGCCTTTCCGGTAGCAGGTCAAAAATTAATTTCTGCAGGCAAAATCCTCA
ATGATGATACTGCTCTCAAAGAATATAAAATTGATGAGAAAAACTTTGTGGTGGTTATGGTGACCAAACCCAAAGCAGTT
TCAACACCAGCACCAGCTACAACTCAGCAGTCAGCTCCCGCCAGCACTACAGCAGTTACTTCCTCCACGGTAACAACTGT
GGCTCAGGCTCCAACCCCTGCCCCTGCTTTGGCGCCCACTTCCACACCATCATCCGTCACTCCAGCATCAGCGACAGCAT
CTCCTGAACCTGCACCTGCTAGTGCAACTAAACAAGAGAAACCAGCAGAAAAGCCAGCAGAGACACCAGTGGCTACTAGC
CCAACATCAACTGACAGTACATCAGGAGATTCTTCTCGGTCAAACCTTTTTGAAGATGCAACAAGTGCACTTGTGACGGG
TCAGTCTTATGAGAATATGGTCACTGAGATCATGTCAATGGGCTATGAACAAAAGCAAGTAATTGCAGCCCTGAGAGCCA
GTTTCAACAACCCTGACAGAGCGGTGGAATATCTTTTAATGGGAATCCCTGGAGATAGAGAAAATCAGGCTGTGGTTGAC
CCCCCTCAAGCAGCTAGTACTGGGGCTCCTCAGTCTTCAGCAGTGGCTGCAACTGCAGCGACTACAACAGCAACGACTAC
AACAACAAGTTCTGGAGGACATCCCCTTGAATTTTTACGGAATCAGCCTCAGTTTCAACAGATGAGACAAATTATTCAAC
AGAATCCTTCCCTGCTCCCAGCGTTACTGCAGCAGATAGGTCGAGAGAATCCTCAATTACTTCAGCAAATTAGCCAACAC
CAGGAGCATTTTATTCAGATGTTAAATGAACCAGTTCAAGAAGCTGGCGGTCAAGGAGGAGGTGGAGGTGGCAGTGGAGG
AATTGCAGAAGCTGGAAGTGGTCATATGAACTATATTCAAGTAACACCTCAGGAAAAAGAAGCTATAGAAAGGTTAAAGG
CATTAGGATTTCCCGAAGGACTTGTGATCCAAGCATATTTTGCTTGTGAGAAGAATGAAAATTTGGCTGCCAATTTTCTT
CTACAGCAAAACTTTGATGAAGAT

Alignment

ORF - retro_cjac_4184 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHVTLKTLQQRTFKIDIDPEEKVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFV
          M.VTLKTLQQ.TFKIDIDPEE.VKALKEK.ESEKGKDAFPVAGQKLI.AGKILNDDTALKEYKIDEKNFV
Retrocopy MQVTLKTLQQQTFKIDIDPEETVKALKEKTESEKGKDAFPVAGQKLISAGKILNDDTALKEYKIDEKNFV

Parental  VVMVTKPKAVSTPAPATTQQSAPASTTAVTSSTVTTVAQAPTPAPALAPTSTPSSVTPASATASPEPAPA
          VVMVTKPKAVSTPAPATTQQSAPASTTAVTSSTVTTVAQAPTPAPALAPTSTPSSVTPASATASPEPAPA
Retrocopy VVMVTKPKAVSTPAPATTQQSAPASTTAVTSSTVTTVAQAPTPAPALAPTSTPSSVTPASATASPEPAPA

Parental  SATKQEKPAEKPAETPVASSPTSTDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQVIAA
          SATKQEKPAEKPAETPVA.SPTSTDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYE..QVIAA
Retrocopy SATKQEKPAEKPAETPVATSPTSTDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEQKQVIAA

Parental  LRASFNNPDRAVEYLLMGIPGDRENQAVVDPPQAASTGAPQSSAVAAAAATTTATTTTTSSGGHPLEFLR
          LRASFNNPDRAVEYLLMGIPGDRENQAVVDPPQAASTGAPQSSAVA..............SGGHPLEFLR
Retrocopy LRASFNNPDRAVEYLLMGIPGDRENQAVVDPPQAASTGAPQSSAVAXXXXXXXXXXXXXXSGGHPLEFLR

Parental  NQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAGGQGGGGGGGSGGIA
          NQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAGGQ.GGGGGGSGGIA
Retrocopy NQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAGGQ-GGGGGGSGGIA

Parental  EAGSGHMNYIQVTPQEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFDED
          EAGSGHMNYIQVTPQEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFDED
Retrocopy EAGSGHMNYIQVTPQEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFDED

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	1.44 RPM	43.80 RPM
SRP051959_heart	1.68 RPM	51.67 RPM
SRP051959_kidney	2.04 RPM	53.54 RPM
SRP051959_liver	1.88 RPM	53.03 RPM
SRP051959_lung	2.54 RPM	45.84 RPM
SRP051959_lymph_node	2.44 RPM	38.04 RPM
SRP051959_skeletal_muscle	2.88 RPM	71.13 RPM
SRP051959_spleen	2.10 RPM	48.03 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4184 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4184 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4184 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877,
Callithrix jacchus	ENSCJAG00000004494	1 retrocopy	retro_cjac_3896,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184 ,
Dasypus novemcinctus	ENSDNOG00000001174	2 retrocopies	retro_dnov_1982, retro_dnov_989,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361,
Homo sapiens	ENSG00000119318	2 retrocopies	retro_hsap_2611, retro_hsap_3754,
Gorilla gorilla	ENSGGOG00000002511	1 retrocopy	retro_ggor_1829,
Loxodonta africana	ENSLAFG00000007533	1 retrocopy	retro_lafr_1109,
Macaca mulatta	ENSMMUG00000014944	2 retrocopies	retro_mmul_1476, retro_mmul_1725,
Nomascus leucogenys	ENSNLEG00000017319	1 retrocopy	retro_nleu_1590,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429,
Otolemur garnettii	ENSOGAG00000014216	1 retrocopy	retro_ogar_3040,
Pongo abelii	ENSPPYG00000019477	2 retrocopies	retro_pabe_2344, retro_pabe_3162,
Pan troglodytes	ENSPTRG00000021229	1 retrocopy	retro_ptro_1760,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401,