RetrogeneDB ID: retro_ptro_1773

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:33276925..33277597(+)
• Located in intron of: ENSPTRG00000014722

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUGT1
• Ensembl ID: ENSPTRG00000005906
• Aliases: None
• Description: None

Sequence

>retro_ptro_1773
TTAGATAGTGCAGATGCTAATTTCAGTGTCTGGATTAAAAGATGTCAAGAAGCTCAGAATGGCCCAGAATCTGATGTGTG
GACTCATCAGTCAAAAATCAGGTATGACTGGTATCAAACAGAATCGCAAGTAGTCATTACACTTATGATCAAGAATGTTC
AAAGAATGATGTAAATGTGGAATTTTCAGAAAAGGAATTGTCTGCTTTGGTTAAACTTCCTTCTGGAGAGGATTACAATT
TGAAACTGGAACTTCATCCTATAATACCAGAACAGAGCACATTTAAAGTAGTTTCAACCAAGATTGAAATTAAACTGAAA
AAGCCAGAGGCTGTGAGATGGGAAAAGCTAGAGGAGCAAGGAGATGTGCCTACACCAAAACAATTCATAGCAGGTGTAAA
GCACCTACATCCATCATCATCTCCTTATACAAGAAATTGGGATAAATTAGTGGGTAAAATCAAAGAAGAAGAAAATAATG
AAAAGTTGGAGGGAGATGCAGCTTTAAACAGATTATTTCAGCAGATCTATTCAGATGGTTCTGATGAAGTGAAATGTGCC
ATGAACAGATCCTTTATGGGAGTCTGATGGTACAGTTTTGAGTACCAGCTGGTCTGATATAGGTAAAAGGAAAGTTGAAA
TCAATCCTGATGATATGGAATGGAAAAAGTAC

Alignment

ORF - retro_ptro_1773 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.91 %
• Parental protein coverage: 61.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ITGADANFSVWIKRCQEAQNGSESEVWTHQSKIKYDWYQTESQVVITLMIKNVQ-KNDVNVEFSEKELSA
          ...ADANFSVWIKRCQEAQNG.ES.VWTHQSKI.YDWYQTESQVVITLMIKNVQ.KNDVNVEFSEKELSA
Retrocopy LDSADANFSVWIKRCQEAQNGPESDVWTHQSKIRYDWYQTESQVVITLMIKNVQ<KNDVNVEFSEKELSA

Parental  LVKLPSGEDYNLKLELLHPIIPEQSTFKVLSTKIEIKLKKPEAVRWEKLEGQGDVPTPKQFVADVKNLYP
          LVKLPSGEDYNLKLEL.HPIIPEQSTFKV.STKIEIKLKKPEAVRWEKLE.QGDVPTPKQF.A.VK.L.P
Retrocopy LVKLPSGEDYNLKLEL-HPIIPEQSTFKVVSTKIEIKLKKPEAVRWEKLEEQGDVPTPKQFIAGVKHLHP

Parental  SSSPYTRNWDKLVGEIKEEEKNEKLEGDAALNRLFQQIYSDGSDEVKRAMNKSFM-ESGGTVLSTNWSDV
          SSSPYTRNWDKLVG.IKEEE.NEKLEGDAALNRLFQQIYSDGSDEVK.AMN.SFM.ES.GTVLST.WSD.
Retrocopy SSSPYTRNWDKLVGKIKEEENNEKLEGDAALNRLFQQIYSDGSDEVKCAMNRSFM>ESDGTVLSTSWSDI

Parental  GKRKVEINPPDDMEWKKY
          GKRKVEIN.PDDMEWKKY
Retrocopy GKRKVEIN-PDDMEWKKY

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	0.18 RPM	9.38 RPM
SRP007412_cerebellum	0.07 RPM	10.07 RPM
SRP007412_heart	0.12 RPM	13.70 RPM
SRP007412_kidney	0.10 RPM	16.76 RPM
SRP007412_liver	0.13 RPM	18.20 RPM
SRP007412_testis	0.42 RPM	66.39 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1773 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1773 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1773 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2628
Gorilla gorilla	retro_ggor_1840

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008606	2 retrocopies	retro_amel_353, retro_amel_896,
Canis familiaris	ENSCAFG00000004823	1 retrocopy	retro_cfam_136,
Callithrix jacchus	ENSCJAG00000003604	1 retrocopy	retro_cjac_310,
Cavia porcellus	ENSCPOG00000003374	1 retrocopy	retro_cpor_110,
Dasypus novemcinctus	ENSDNOG00000002991	1 retrocopy	retro_dnov_2621,
Homo sapiens	ENSG00000165416	1 retrocopy	retro_hsap_2628,
Gorilla gorilla	ENSGGOG00000006797	1 retrocopy	retro_ggor_1840,
Nomascus leucogenys	ENSNLEG00000015700	1 retrocopy	retro_nleu_640,
Otolemur garnettii	ENSOGAG00000008220	1 retrocopy	retro_ogar_41,
Pan troglodytes	ENSPTRG00000005906	1 retrocopy	retro_ptro_1773 ,