RetrogeneDB ID: retro_ptro_6

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:45066938..45067931(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000005844
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CALU
• Ensembl ID: ENSPTRG00000019668
• Aliases: None
• Description: Pan troglodytes calumenin (CALU), mRNA. [Source:RefSeq mRNA;Acc:NM_001246592]

Sequence

>retro_ptro_6
ATGGCGGGCGGTGGCCGCGGCCGCCACCTGGGGTTAGCCCTGGGGCTGCTGCTGGCGCTGGTGCTGGCACCGCGGGTTCT
GCGGGCCAAGCCCACGGTGCGCAAAGAGTGCGTGGTGCGGCCCGACTCGGAGCTGGGCGAGCGGCCCCCTGAGGACAACC
AGAGCTTCCAGTACGACCACGAGGCCTTCCTGGGCAAGGAGGACTCCAAGACCTTCGACCAGCTCACCCCGGACGAGAGC
AAGGAGAGGCTAGGGAAGATTGTTGATCGAATCGACAATGATGGGGATGGCTTTGTCACTACTGAGGAGCTGAAAACCTG
GATCAAACGGGTGCAGAAAAGATACATCTTTGATAATGTCGCCAAAGTCTGGAAGGATTATGATAGGGACAAGGTTGATA
AAATTTCCTGGGAAGAATACAAACAAGCCACCTATGGTTACTACCTAGGAAACCCCGCAGAGTTTCATGATTCTTCAGAT
CATCACACCTTTAAAAAGATGCTGCCACGTGATGAGAGAAGATTCAAAGCTGCAGACCTCAATGGTGACCTGACAGCTAC
TCGGGAGGAGTTCACTGCCTTTCTGCATCCTGAAGAGTTTGAACATATGAAGGAAATTGTGGTTTTGGAAACCCTAGAGG
ACATCGACAAGAACGGGGATGGGTTTGTGGATCAGGATGAGTATATTGCGGATATGTTTTCCCATGAGGAGAATGGCCCT
GAGCTAGACTGGGTTTTATCAGAACGGGAGCAGTTTAACGAATTCCAGGATCTGAACAAGGACGGGAAGTTAGACAAAGA
TGAGATTCGCCACTGGATCCTCCCTCAAGATTATGATCATGCACAGGCTGAGGCCAGGCATCTGGTATATGAGTCAGACA
AAAACAAGGATGAGAAGCTAACTAAAGAGGAAATATTGGAGAACTGGAACATGTTTGTTGGAAGCCAAGCTACCAATTAC
GGGGAAGATCTCACAAAAAATCATGATGAGCTT

Alignment

ORF - retro_ptro_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.19 %
• Parental protein coverage: 97.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LMCLSLCTAFALSKPTEKKDRV-HHEPQLSDKVHNDAQSFDYDHDAFLGAEEAKTFDQLTPEESKERLGK
          L..L.L.......KPT..K..V......L......D.QSF.YDH.AFLG.E..KTFDQLTP.ESKERLGK
Retrocopy LLALVLAPRVLRAKPTVRKECVVRPDSELGERPPEDNQSFQYDHEAFLGKEDSKTFDQLTPDESKERLGK

Parental  IVSKIDGDKDGFVTVDELKDWIKFAQKRWIYEDVERQWKGHDLNEDGLVSWEEYKNATYGYVLDDP----
          IV..ID.D.DGFVT..ELK.WIK..QKR.I...V...WK..D.......SWEEYK.ATYGY.L..P....
Retrocopy IVDRIDNDGDGFVTTEELKTWIKRVQKRYIFDNVAKVWKDYDRDKVDKISWEEYKQATYGYYLGNPAEFH

Parental  DPDDGFNYKQMMVRDERRFKMADKDGDLIATKEEFTAFLHPEEYDYMKDIVVQETMEDIDKNADGFIDLE
          D..D....K.M..RDERRFK.AD..GDL.AT.EEFTAFLHPEE...MK.IVV.ET.EDIDKN.DGF.D..
Retrocopy DSSDHHTFKKMLPRDERRFKAADLNGDLTATREEFTAFLHPEEFEHMKEIVVLETLEDIDKNGDGFVDQD

Parental  EYIGDMYSHDGNTDEPEWVKTEREQFVEFRDKNRDGKMDKEETKDWILPSDYDHAEAEARHLVYESDQNK
          EYI.DM.SH..N..E..WV..EREQF.EF.D.N.DGK.DK.E...WILP.DYDHA.AEARHLVYESD.NK
Retrocopy EYIADMFSHEENGPELDWVLSEREQFNEFQDLNKDGKLDKDEIRHWILPQDYDHAQAEARHLVYESDKNK

Parental  DGKLTKEEIVDKYDLFVGSQATDFGEALVR-HDE
          D.KLTKEEI......FVGSQAT..GE.L...HDE
Retrocopy DEKLTKEEILENWNMFVGSQATNYGEDLTKNHDE

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	8.33 RPM	43.61 RPM
SRP007412_cerebellum	9.25 RPM	46.39 RPM
SRP007412_heart	8.16 RPM	246.63 RPM
SRP007412_kidney	6.33 RPM	64.25 RPM
SRP007412_liver	12.14 RPM	120.69 RPM
SRP007412_testis	22.34 RPM	62.60 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_6 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_6 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_6 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010477	1 retrocopy	retro_dnov_863,
Pongo abelii	ENSPPYG00000017982	1 retrocopy	retro_pabe_211,
Pan troglodytes	ENSPTRG00000019668	1 retrocopy	retro_ptro_6 ,