RetrogeneDB ID: retro_ptro_2751

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:52264940..52265474(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC11A
• Ensembl ID: ENSPTRG00000007404
• Aliases: None
• Description: None

Sequence

>retro_ptro_2751
ATACTGTCTCTAGACTTTTTGGATGATGTGCAGTGGATGAACAAGTGGCAGCTCTATTATCAAGTCCTAAATTTTGGAAT
GATTGTCTCATCAGCACTCATGATCTGGAAGGGGTTAATGGTAATAACTGGAAGTGAAAGTCCAATTGAGTTGCTCAGTG
GCAGCATGGAACCTGCATTTCACAGAGGATATCTTCTCTTTCTAACAAATCGAGTTGAAGATCCCATACGAGTGGGAGAA
ATTGCTGTTCTAAGGATAGAAGGAAGAAAGATTCCTATAGTTCACCGAGTCTTGAAGATTCATGAAAAGCAAAATGGGCA
TATCAAGTTTTTGACCAAAGGAGATAATAATGCGGTTGATGACAGAGGCCTCTATAAACAAGATCAACATTGGCTAGAGA
AAAAAGATGTCGTGGGGAGAGCCAGGGGATTTGTTCCTTATATTGGAATTGGGACGAGCCTCATGAATGACTATCCTAAA
TTTAAGTATGAAGTGCTCTTTTTGCTGGGTTTATTTGTGCTGGTCCATCGTGAG

Alignment

ORF - retro_ptro_2751 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLSLDFLDDVRRMNKRQLYYQVLNFGMIVSSALMIWKGLMVITGSESPIVVVLSGSMEPAFHRGDLLFLT
          .LSLDFLDDV..MNK.QLYYQVLNFGMIVSSALMIWKGLMVITGSESPI...LSGSMEPAFHRG.LLFLT
Retrocopy ILSLDFLDDVQWMNKWQLYYQVLNFGMIVSSALMIWKGLMVITGSESPIEL-LSGSMEPAFHRGYLLFLT

Parental  NRVEDPIRVGEIVVFRIEGREIPIVHRVLKIHEKQNGHIKFLTKGDNNAVDDRGLYKQGQHWLEKKDVVG
          NRVEDPIRVGEI.V.RIEGR.IPIVHRVLKIHEKQNGHIKFLTKGDNNAVDDRGLYKQ.QHWLEKKDVVG
Retrocopy NRVEDPIRVGEIAVLRIEGRKIPIVHRVLKIHEKQNGHIKFLTKGDNNAVDDRGLYKQDQHWLEKKDVVG

Parental  RARGFVPYIGIVTILMNDYPKFKYAVLFLLGLFVLVHRE
          RARGFVPYIGI.T.LMNDYPKFKY.VLFLLGLFVLVHRE
Retrocopy RARGFVPYIGIGTSLMNDYPKFKYEVLFLLGLFVLVHRE

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	13.14 RPM
SRP007412_cerebellum	0.00 RPM	20.72 RPM
SRP007412_heart	0.06 RPM	50.13 RPM
SRP007412_kidney	0.03 RPM	64.36 RPM
SRP007412_liver	0.00 RPM	60.00 RPM
SRP007412_testis	0.11 RPM	73.03 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2751 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2751 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2751 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4058
Gorilla gorilla	retro_ggor_2726
Pongo abelii	retro_pabe_3333
Macaca mulatta	retro_mmul_2343

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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,