RetrogeneDB ID: retro_cjac_2904

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:81609540..81610245(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AHSA2
• Ensembl ID: ENSCJAG00000034768
• Aliases: None
• Description: None

Sequence

>retro_cjac_2904
AATGCCACCAGCTGGTCCAAAGGGAAGCTCCAGGAGCTCCTGGTGGGCATCGTTGTGGAGGATGAAGCCGGCCGCTGAGA
AATCAGTGAGCTGAAGCAGGTGGGAGGTCAGGCTTCTTGCAGCAGCTGCAAAGCAAAGCTGATTTTTTTCTATTAGTGGA
ACATCAAACTGGGCTAGAAAGATATCATTAAAGAATCTGATGTGAAGCACAAGGGATTGATTGAAATACCTAATCTTTCT
GAAGACAATAAAGTAGACAATACTAAGGTGAACATGAGTAAAAAGAAAGGAGATGGGGATACACTGCAGGATCTTATGAA
AACTGCAGGCACTGCCAAGGTTAGGGAGGAGGTCCTTGGAGATTACTGGAAGGCACTTAAAACAAAATTTACAATGGGAA
TGGCTTTACCAATGAAAACTATGGCAACCTAGGAATTGACTGTTAACATAAAACGGAGGGAGAATATCTTCCAGGTTCAG
GCCTCATCTCGAGTGTCACTGGGTGTAAGGATTCCCACTGTGACTCTTCCCATGAGGGAACAGTTTGACACAACTGTAGA
GCAGCTGTAAAGCATCTTCATTGTGAAGGATTTGGTGCAAAAATTTTCTAAATCTCCTGCTGTATTAGAAGCTGAAAAGG
GAGGGAAATTCCAAATGTTTGATGGGAACATCACTGATGAATGTACAGAATTATTAACCAAAAAA

Alignment

ORF - retro_cjac_2904 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.89 %
• Parental protein coverage: 69.7 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NATSWSKGKLQELLVGIVVENETGRGEISERKQVEGEASCSSRKGKLIFLYEWNIKLDWKGILKESGVKH
          NATSWSKGKLQELLVGIVVE.E.GR.EISE.KQV.G.ASCSS.K.KLIF.Y.WNIKL..K.I.KES.VKH
Retrocopy NATSWSKGKLQELLVGIVVEDEAGR*EISELKQVGGQASCSSCKAKLIFFY*WNIKLG*KDIIKESDVKH

Parental  KGLIEIPNLSEENE-DDTEVNVSKKKGDGDILKDLMKTAGTAKVR-EALGDYLKALKMEFTVGMILPTKS
          KGLIEIPNLSE.N..D.T.VN.SKKKGDGD.L.DLMKTAGTAKVR.E.LGDY.KALK..FT.GM.LP.K.
Retrocopy KGLIEIPNLSEDNKVDNTKVNMSKKKGDGDTLQDLMKTAGTAKVREEVLGDYWKALKTKFTMGMALPMKT

Parental  MATQELTGKRKLSEN--TLQASSPVVLGVRIPSVALRMMELFDTTV-VLYSIFTVKDLVQKFSKSTAVLE
          MAT.ELT...K..EN....QASS.V.LGVRIP.V.L.M.E.FDTTV..L.SIF.VKDLVQKFSKS.AVLE
Retrocopy MAT*ELTVNIKRRENIFQVQASSRVSLGVRIPTVTLPMREQFDTTVEQL*SIFIVKDLVQKFSKSPAVLE

Parental  AEKGGKFQMFDGNITGEYLELLANK
          AEKGGKFQMFDGNIT.E..ELL..K
Retrocopy AEKGGKFQMFDGNITDECTELLTKK

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	0.00 RPM	4.42 RPM
SRP051959_heart	0.00 RPM	5.24 RPM
SRP051959_kidney	0.00 RPM	3.00 RPM
SRP051959_liver	0.00 RPM	3.01 RPM
SRP051959_lung	0.02 RPM	11.00 RPM
SRP051959_lymph_node	0.00 RPM	13.47 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.75 RPM
SRP051959_spleen	0.00 RPM	8.99 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2904 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2904 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2904 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034768	1 retrocopy	retro_cjac_2904 ,
Equus caballus	ENSECAG00000005107	1 retrocopy	retro_ecab_217,
Gorilla gorilla	ENSGGOG00000014565	1 retrocopy	retro_ggor_237,
Pongo abelii	ENSPPYG00000012385	1 retrocopy	retro_pabe_471,
Pan troglodytes	ENSPTRG00000023268	1 retrocopy	retro_ptro_144,
Tursiops truncatus	ENSTTRG00000013366	1 retrocopy	retro_ttru_1173,