RetrogeneDB ID: retro_cjac_4008

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL287992.1:6226..7238(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FECH
• Ensembl ID: ENSCJAG00000003873
• Aliases: None
• Description: Ferrochelatase [Source:UniProtKB/TrEMBL;Acc:F6T667]

Sequence

>retro_cjac_4008
ATGCTTTCACTCGGCCCAACCATGGCTGCGGCCCTGCGCGCCGCGGGCGCCCTGCTCCGGGATCCGCTGGCGTCCGGCAG
CTGGAGGGCCGGTCAACAGCGGAGGTGGAAGTGGCTGCAGCCGCAGCAGCTGCCGCTGCAGAAACAACCCAGCATGCCTG
GGCCGCAAAGCCTCAAGTTCAGCCGGAGAAGAGGAAGCCAAAAACTGGAATATTAATGCTAAACATGGGAGGCCCTGAAA
CCCTTGGAGATGTTCACGGCTTCCTTCTGAGACTCTTCTTGGACCGAGATCTCATGATGCTTCCTATTCAGAATAAGCAA
TGAATGGCACCATTCATTGCCAAACGCCGAACCCCCAAGATTCAAGAGCAGTACCGCAGGATTGGAGGCGGATCCCCCAT
CAAGATGTAGACTTCCAAGCAGGGAGAGGGCGTGGTGAAGCTGCTGGATGAATTGTCCCCCAACACAGCCCCTCACAAAT
ACTATATTGGATTTCGGTATGTCCATCCTTTAACAGAAGAAGCAATTGAAGAGATGGAGAGAGACGGCCTAGAAAGGGCT
ATTGCTTTCACGCAGTATCCACAGTACAGCTGCTCCACCACAGGCAGCAGCCGAAATGCCATTTACATATACTATAATCA
AGTGGGACGGAAGCCCATGATGAAGTGGCGCACTATTGACAGGTGGCCCACACATCGCCTCCTCATTCAATGCTTTGCAG
ACCACATTCTAAAGGAATTGGACCATTTTCCACTTGAGAAGAGAATCGAGGTGGTCATTCCGTTTTCTGCTCACTCACTG
CCAATGTCCGTGGTCAACAGAGTGACCCGTATCCTCAGGAGGTGAGCGCCACTGTCCAAAAGGTCATGGAAAGGCTGGAG
TACTGCAACCCCTTCCGACTGGTGTGGCAATCCAAGGTTGGTCCAATGCCCTGGTTAGGTTCTCAAACAGATGAATCTAT
CAAAGGACTCTGTGAGAGGGGGAGGAAGAATATCCTCTTGGTTCCGATAGCA

Alignment

ORF - retro_cjac_4008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.08 %
• Parental protein coverage: 79.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLSLGPNMAAALRAAGALLRDPLVSGSWRACQPWRWK-SGAAAAAATAETAQHALGAKPQVQSEKRKPKT
          MLSLGP.MAAALRAAGALLRDPL.SGSWRA.Q..RWK...AAAAAA.AET.QHA..AKPQVQ.EKRKPKT
Retrocopy MLSLGPTMAAALRAAGALLRDPLASGSWRAGQQRRWK<VAAAAAAAAAETTQHAWAAKPQVQPEKRKPKT

Parental  GILMLNMGGPETLGDVHDFLLRLFLDRDLMTLPIQNK--LAPFIAKRRTPKIQEQYRRIGGGSPIKMWTS
          GILMLNMGGPETLGDVH.FLLRLFLDRDLM.LPIQNK...APFIAKRRTPKIQEQYRRIGGGSPIKM.TS
Retrocopy GILMLNMGGPETLGDVHGFLLRLFLDRDLMMLPIQNKQ*MAPFIAKRRTPKIQEQYRRIGGGSPIKM*TS

Parental  KQGEGMVKLLDELSPNTVIKKITHSVYHGVWYVHPLTEEAIEEMERDGLERAIAFTQYPQYSCSTTGSSL
          KQGEG.VKLLDELSPNT......H..Y.G..YVHPLTEEAIEEMERDGLERAIAFTQYPQYSCSTTGSS.
Retrocopy KQGEGVVKLLDELSPNTA----PHKYYIGFRYVHPLTEEAIEEMERDGLERAIAFTQYPQYSCSTTGSSR

Parental  NAIYRYYNQVGRKPVMKWSTIDRWPTHRLLIQCFADHILKELDHFPLEKRSEVVILFSAHSLPMSVVNR-
          NAIY.YYNQVGRKP.MKW.TIDRWPTHRLLIQCFADHILKELDHFPLEKR.EVVI.FSAHSLPMSVVNR.
Retrocopy NAIYIYYNQVGRKPMMKWRTIDRWPTHRLLIQCFADHILKELDHFPLEKRIEVVIPFSAHSLPMSVVNR<

Parental  GDPYPQEVSATVQKVMERLGYCNPFRLVWQSKVGPMPWLGPQTDESIKGLCERGRKNILLVPIA
          .DPYPQEVSATVQKVMERL.YCNPFRLVWQSKVGPMPWLG.QTDESIKGLCERGRKNILLVPIA
Retrocopy SDPYPQEVSATVQKVMERLEYCNPFRLVWQSKVGPMPWLGSQTDESIKGLCERGRKNILLVPIA

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	0.33 RPM	4.48 RPM
SRP051959_heart	1.26 RPM	11.07 RPM
SRP051959_kidney	0.84 RPM	8.99 RPM
SRP051959_liver	1.02 RPM	8.51 RPM
SRP051959_lung	0.62 RPM	5.81 RPM
SRP051959_lymph_node	0.34 RPM	4.73 RPM
SRP051959_skeletal_muscle	1.48 RPM	14.61 RPM
SRP051959_spleen	0.95 RPM	10.44 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4008 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4008 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4008 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	ENSCJAG00000003873	1 retrocopy	retro_cjac_4008 ,
Homo sapiens	ENSG00000066926	1 retrocopy	retro_hsap_2631,
Gorilla gorilla	ENSGGOG00000005554	1 retrocopy	retro_ggor_1841,
Macaca mulatta	ENSMMUG00000022568	1 retrocopy	retro_mmul_1485,
Nomascus leucogenys	ENSNLEG00000008062	1 retrocopy	retro_nleu_643,
Oryctolagus cuniculus	ENSOCUG00000003020	1 retrocopy	retro_ocun_497,
Pongo abelii	ENSPPYG00000009182	1 retrocopy	retro_pabe_2332,
Pan troglodytes	ENSPTRG00000010045	1 retrocopy	retro_ptro_1776,