RetrogeneDB ID: retro_cjac_1496

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:7479291..7479815(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC11A
• Ensembl ID: ENSCJAG00000016146
• Aliases: None
• Description: SEC11 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:17718]

Sequence

>retro_cjac_1496
GTAAACAGTATGCGGCGGATGAACAAGCGGCAGCTCTATTATCAAGTCCTAAATTTCGGAATGATTGTCTTATCAGCACT
AATGATCTGAAAGAGGTTAATGGTAATAACTAGAAGTGAAAGTCCAATTGTAACTGTAGTGGTTCTCGGTGGCAACATGG
AACCTGCATTTCATACAGAAAATCTTCTCTTTCTAACAAATCAAGTTGAAGATCCTAGATGAGCGGGAAAAATCATTGTT
TTTAGGATGGAAGGAAGAGAGATTCCTGTAGTTCACTGAGACTTGAAGATTCATGAAATGCAAAATGGGCATATCAAGTT
TTTGACTGAAGGAGATAATGATGCGCTTAATGACTGAAGCCTCTATAAACAAGGAAGAATTGGCTAGAGAAAAAAGATGT
TATGGGAAGAGCCGGGGAATTTGTTCCTGATACGGGAATAGTGACTATCCTCATGAATGACTATCCTAAATTTACGTATG
CAGTGCTCTTTTTGCTTGATTTATTTGTGCTGGTCCACCGTGAA

Alignment

ORF - retro_cjac_1496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.14 %
• Parental protein coverage: 96.65 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LDDVRRMNKRQLYYQVLNFGMIVSSALMIWKGLMVITGSESPIV--VVLSGSMEPAFHRGDLLFLTNRVE
          ....RRMNKRQLYYQVLNFGMIV.SALMI.K.LMVIT.SESPIV..VVL.G.MEPAFH...LLFLTN.VE
Retrocopy VNSMRRMNKRQLYYQVLNFGMIVLSALMI*KRLMVITRSESPIVTVVVLGGNMEPAFHTENLLFLTNQVE

Parental  DPIRVGEIVVFRIEGREIPIVHRVLKIHEKQNGHIKFLTKGDNNAVDDRGLYKQG-QHWLEKKDVVGRAR
          DP...G.I.VFR.EGREIP.VH..LKIHE.QNGHIKFLT.GDN.A..D..LYKQG...WLEKKDV.GRA.
Retrocopy DPR*AGKIIVFRMEGREIPVVH*DLKIHEMQNGHIKFLTEGDNDALND*SLYKQG<KNWLEKKDVMGRAG

Parental  GFVPYIGIVTILMNDYPKFKYAVLFLLGLFVLVHRE
          .FVP..GIVTILMNDYPKF.YAVLFLL.LFVLVHRE
Retrocopy EFVPDTGIVTILMNDYPKFTYAVLFLLDLFVLVHRE

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	14.38 RPM
SRP051959_heart	0.02 RPM	11.14 RPM
SRP051959_kidney	0.00 RPM	18.97 RPM
SRP051959_liver	0.00 RPM	16.35 RPM
SRP051959_lung	0.00 RPM	14.79 RPM
SRP051959_lymph_node	0.00 RPM	15.57 RPM
SRP051959_skeletal_muscle	0.00 RPM	12.08 RPM
SRP051959_spleen	0.00 RPM	15.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1496 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1496 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1496 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012889	1 retrocopy	retro_cfam_1416,
Callithrix jacchus	ENSCJAG00000016146	1 retrocopy	retro_cjac_1496 ,
Felis catus	ENSFCAG00000029786	2 retrocopies	retro_fcat_1178, retro_fcat_1908,
Homo sapiens	ENSG00000140612	1 retrocopy	retro_hsap_4058,
Gorilla gorilla	ENSGGOG00000011129	1 retrocopy	retro_ggor_2726,
Monodelphis domestica	ENSMODG00000019364	1 retrocopy	retro_mdom_726,
Pongo abelii	ENSPPYG00000006881	1 retrocopy	retro_pabe_3333,
Pan troglodytes	ENSPTRG00000007404	1 retrocopy	retro_ptro_2751,
Tupaia belangeri	ENSTBEG00000012320	3 retrocopies	retro_tbel_1139, retro_tbel_2280, retro_tbel_745,
Tursiops truncatus	ENSTTRG00000005833	1 retrocopy	retro_ttru_1237,