RetrogeneDB ID: retro_ptro_1609

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:71767368..71767928(-)
• Located in intron of: ENSPTRG00000012035

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOBKL3
• Ensembl ID: ENSPTRG00000012775
• Aliases: MOBKL3, HSPE1, MOB4, PREI3
• Description: None

Sequence

>retro_ptro_1609
ATGATCATGGCAGAGGGGATGGCAGTGCTGAGGCAGAACAGGCAGGGCACCAAGGCACAGGATATCTATAATTGGCCTGA
TGAATCCTTTGATAAAATGGACAGTACACTAGCTGCTCAACAGTCTATTCAACAGAACATAAGAGCAGATTGCTCCAATA
TTGACAAAATTCTTGAAGCACCTAAAGGCCAAGATGAAGGTGTATGGAAGTATGACATTTAAGACAATTGTGCCTTGAGC
TAATTGGACTTGCTGTCAAACTTCAGAGTGAATGCCATCCAGATACTTGTACTCAAATGACAGCAACTGAACAATGGATT
TTTCTTTGCGTAGCTCATAAAACTCCAAAAGAGTGTCCTGCTATAGACTATACTAGACACACACCTGATGGTGCTGCATG
TCTTCTGAATAGCAATAAATATTTTCCCAGCAGGGTTAGCATAAAGGAATCATCTGTAGTGACACCAAAATCAGTATGCC
GTAGAATTTACAGAATATTTTCACATGTTTATTTTCATCATTGGCAGATATTTGATGAATATGAAAATGAAACATTTGTG

Alignment

ORF - retro_ptro_1609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.77 %
• Parental protein coverage: 83.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVMAEGTAVLRRNRPGTKAQDFYNWPDESFDEMDSTLAVQQYIQQNIRADCSNIDKILEPPEGQDEGVWK
          M.MAEG.AVLR.NR.GTKAQD.YNWPDESFD.MDSTLA.QQ.IQQNIRADCSNIDKILE.P.GQDEGVWK
Retrocopy MIMAEGMAVLRQNRQGTKAQDIYNWPDESFDKMDSTLAAQQSIQQNIRADCSNIDKILEAPKGQDEGVWK

Parental  YE-HLRQFCLELNGLAVKLQSECHPDTCTQMTATEQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSN
          Y..HLRQ.CLEL.GLAVKLQSECHPDTCTQMTATEQWIFLC.AHKTPKECPAIDYTRHT.DGAACLLNSN
Retrocopy YD<HLRQLCLELIGLAVKLQSECHPDTCTQMTATEQWIFLCVAHKTPKECPAIDYTRHTPDGAACLLNSN

Parental  KYFPSRVSIKESSVAKLGSVCRRIYRIFSHAYFHHRQIFDEYENETFL
          KYFPSRVSIKESSV....SVCRRIYRIFSH.YFHH.QIFDEYENETF.
Retrocopy KYFPSRVSIKESSVVTPKSVCRRIYRIFSHVYFHHWQIFDEYENETFV

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	0.02 RPM	27.65 RPM
SRP007412_cerebellum	0.00 RPM	21.44 RPM
SRP007412_heart	0.00 RPM	27.02 RPM
SRP007412_kidney	0.00 RPM	14.25 RPM
SRP007412_liver	0.00 RPM	7.20 RPM
SRP007412_testis	0.00 RPM	8.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1609 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1609 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1609 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2275

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000000932	1 retrocopy	retro_etel_952,
Latimeria chalumnae	ENSLACG00000015430	1 retrocopy	retro_lcha_112,
Monodelphis domestica	ENSMODG00000012305	2 retrocopies	retro_mdom_1333, retro_mdom_963,
Nomascus leucogenys	ENSNLEG00000006881	2 retrocopies	retro_nleu_287, retro_nleu_376,
Oryctolagus cuniculus	ENSOCUG00000005712	1 retrocopy	retro_ocun_30,
Pan troglodytes	ENSPTRG00000012775	3 retrocopies	retro_ptro_1609 , retro_ptro_626, retro_ptro_640,
Sarcophilus harrisii	ENSSHAG00000017821	1 retrocopy	retro_shar_351,
Sus scrofa	ENSSSCG00000016079	2 retrocopies	retro_sscr_804, retro_sscr_824,
Tarsius syrichta	ENSTSYG00000001726	1 retrocopy	retro_tsyr_1673,