RetrogeneDB ID: retro_cjac_3817

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284783.1:5159..6008(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISYNA1
• Ensembl ID: ENSCJAG00000014230
• Aliases: None
• Description: None

Sequence

>retro_cjac_3817
ATGGAGGCCGCCGCCCAGTTCTTCTTCGAGAGCCCGGACGTGGTCTACGGCCCGAGGCTATCGAGGCGCAATACGAATAC
CGGAAGACGCGCCTCAGCTGCGAGGGCAGCGTCCTCAAGGTGCACCCCACGACCACACGCTTCACCTTCCGGACCGTCCG
GCAGGTGCCCAGGCTTGGGGTCATGCTTGTCGGCTGGGGCAGGAACAATGGCTCCACGCTCACAGCCGCGGTGCTGGCCA
AACTACTGCATCTGTCCTGGCCCATGCGCAGCGGCCACAAGGAGGTCAACTACTAGGGCTCACTGACTCAGGCAGGCACC
GTGAGCCTGGGCTTGGACGCCGAGGGCCAGGAGGTGTTCGTGCCCTTTAGTGCGCTGCTGCCCATGGTGGCTCCCAACTA
CCTCGTGTTTGATGGCTGGGACATCTCATTGCTGAACCTCGCCGAGGCTATGCGGCGCGTGAAGGTGCTGGATTGGGAGC
TGCAGGAGCAACTGTGGCCGCACATGGAAGCCCTGCGGCCTCGGCCTTCCGTCTACATCCCCAAGTTCATCGCCACCAAC
CAGAGAACGCACGCGGACAACCTCATCCCGGGCTCGTGCGAGCAGCAGCTGGAGCAGATCCGCAAGGACATCCGACACTT
CCGGTCTAGCGCGGGGCTCGACAAAGTCATCGTGCTGTTGACGGCCAACACAGAGGGCCTTCTGTGAGGTGGTTCCAGGC
CTCAACGACAGGGCTGAGAACCTGCTGCGCACCATTGAGCTTGGCCTGGAGGTATCTCCCTCTACGCTCTTCGCCGTTGC
CAGCATCCTGGAGGGCTGTGCCTTCCTCACTGGGTCCCTGCAGAACACC

Alignment

ORF - retro_cjac_3817 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.77 %
• Parental protein coverage: 50.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEAAAQFFVESPDVVYGP-EAIEAQYEYRTTRVSREGGVLKVHPTTTRFTFRTVRQVPRLGVMLVGWGGN
          MEAAAQFF.ESPDVVYGP.EAIEAQYEYR.TR.S.EG.VLKVHPTTTRFTFRTVRQVPRLGVMLVGWG.N
Retrocopy MEAAAQFFFESPDVVYGP<EAIEAQYEYRKTRLSCEGSVLKVHPTTTRFTFRTVRQVPRLGVMLVGWGRN

Parental  NGSTLTAAVLANRLRLSWPTRSGRKEANYYGSLTQAGTVSLGLDAEGQEVFVPFSALLPMVAPNDLVFDG
          NGSTLTAAVLA..L.LSWP.RSG.KE.NY.GSLTQAGTVSLGLDAEGQEVFVPFSALLPMVAPN.LVFDG
Retrocopy NGSTLTAAVLAKLLHLSWPMRSGHKEVNY*GSLTQAGTVSLGLDAEGQEVFVPFSALLPMVAPNYLVFDG

Parental  WDISSMNLAEAMRRAKVLDWELQEQLWPHMEALRPRPSVYIPEFIAANQSTRADNLIPGSRAQQLEQIRK
          WDIS..NLAEAMRR.KVLDWELQEQLWPHMEALRPRPSVYIP.FIA.NQ.T.ADNLIPGS..QQLEQIRK
Retrocopy WDISLLNLAEAMRRVKVLDWELQEQLWPHMEALRPRPSVYIPKFIATNQRTHADNLIPGSCEQQLEQIRK

Parental  DIRDFRSSAGLDKVVVLWTANTE-RFCEVVPGLNDTAENLLRTIELGLEVSPSTLFAVASILEGCAFLNG
          DIR.FRSSAGLDKV.VL.TANTE..FCEVVPGLND.AENLLRTIELGLEVSPSTLFAVASILEGCAFL.G
Retrocopy DIRHFRSSAGLDKVIVLLTANTE>AFCEVVPGLNDRAENLLRTIELGLEVSPSTLFAVASILEGCAFLTG

Parental  SPQNT
          S.QNT
Retrocopy SLQNT

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	0.02 RPM	0.55 RPM
SRP051959_heart	0.02 RPM	2.49 RPM
SRP051959_kidney	0.04 RPM	2.64 RPM
SRP051959_liver	0.11 RPM	0.93 RPM
SRP051959_lung	0.52 RPM	7.01 RPM
SRP051959_lymph_node	1.35 RPM	11.21 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.76 RPM
SRP051959_spleen	0.23 RPM	5.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3817 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3817 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3817 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014230	6 retrocopies	retro_cjac_2768, retro_cjac_2803, retro_cjac_2809, retro_cjac_2831, retro_cjac_3817 , retro_cjac_435,
Homo sapiens	ENSG00000105655	1 retrocopy	retro_hsap_2918,
Gorilla gorilla	ENSGGOG00000016939	1 retrocopy	retro_ggor_2019,
Nomascus leucogenys	ENSNLEG00000006026	1 retrocopy	retro_nleu_826,