RetrogeneDB ID: retro_ggor_3040

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:83247083..83248042(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STIP1
• Ensembl ID: ENSGGOG00000012132
• Aliases: None
• Description: None

Sequence

>retro_ggor_3040
GAAGCAGGCACTGAAAGAAAAAGAGCTGAGGAACGATGCCTACAAGAAGAAAGACTGACAGCCTTGAAGCATTACGACAA
AGCCAGGGAGCTGGACCCCAGCAACATGACTTACATTACCAATCAAGCAGCAGTATACTTTGAAAAGGGCAACTACAATA
AGTGCTGGGAGCTTTGTGAGAAGTCCATTGAAATGGGGAGAGAAAACAGAGAAGACTATCTACAGATTGCCAAAGTGTGT
GCTCGAATTGGCAACTCCTACTTCAAAGAAGAAAAGTACAAGGATGCCGTCCATTTCTATAACAAGTCTCTGGCAGAGCA
CCGAACTCCAGATGTGCTCAAGAAATGCCAGCAGGCAGAGAAAATCCTGAAGGAGCAAGAACGGCTGGCCTACATAAACC
CCGACCTGGCTTTAGAGGAGAAAACAAAGGCAACGAGTGTTTTCAGAAAGGGGACTATCCCCACGCCATGAAGCATTATA
CGGAAGCCATCAAAAGGAACCCGAAAGATGCCAAATTATACAGCAATCGAGCTGCCTGTTACACCAAACTCCTGGATTCC
AGCTGGCACTCAAGGACTGTGAAGAATGTATCCAGCTAGAACCGACTTTCATCAAGGGTTATACACGGAAAGCCGTTGCC
CTGGAAGTGATGAAGGACTACACCAAAGTCATGGATCTGTACCGGAAGGTGCTAGACCCGGACTCCAGCTGTAAGGAGGC
GGCAGGCGGCTACCAGCGCTGTATGATGGCGCAGTACAACCGGCACCGCAGCCCCGAAGATGTGAAGCGAAGAGCCATGG
CCGACCCCGAGGTGCAGCAGATCATGAGTGACATAGCCATGCACCTTATCCTGGAGCAGATGCAGAAGGACCCCCCAGGC
ACTCAGCGAACACCTAAAGAATCCTGTAATCGCAAAGAAGATCCAGAAGCTGATGGATGTGGGTCTGATTGCAATTCGA

Alignment

ORF - retro_ggor_3040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.07 %
• Parental protein coverage: 54.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QALKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENR
          .A..E..............TALKHYDKA.ELDP.NMTYITNQAAVYFEKG.YNKC.ELCEK.IE.GRENR
Retrocopy EAGTERKRAEERCLQEERLTALKHYDKARELDPSNMTYITNQAAVYFEKGNYNKCWELCEKSIEMGRENR

Parental  EDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKILKEQERLAYINPDLALEE
          EDY.QIAK..ARIGNSYFKEEKYKDA.HFYNKSLAEHRTPDVLKKCQQAEKILKEQERLAYINPDLALEE
Retrocopy EDYLQIAKVCARIGNSYFKEEKYKDAVHFYNKSLAEHRTPDVLKKCQQAEKILKEQERLAYINPDLALEE

Parental  K-NKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLE-FQLALKDCEECIRLEPTFIKGY
          K.NKGNECFQKGDYP.AMKHYTEAIKRNPKDAKLYSNRAACYTKLL..FQLALKDCEECI.LEPTFIKGY
Retrocopy K<NKGNECFQKGDYPHAMKHYTEAIKRNPKDAKLYSNRAACYTKLLD<FQLALKDCEECIQLEPTFIKGY

Parental  TRKAAALEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQYNRHDSPEDVKRRAMADPEVQQIMSD
          TRKA.ALE.MKDYTK.MD.Y.K.LD.DSSCKEAA.GYQRCMMAQYNRH.SPEDVKRRAMADPEVQQIMSD
Retrocopy TRKAVALEVMKDYTKVMDLYRKVLDPDSSCKEAAGGYQRCMMAQYNRHRSPEDVKRRAMADPEVQQIMSD

Parental  PAMRLILEQMQKD-PQALSEHLKNPVIAQKIQKLMDVGLIAIR
          .AM.LILEQMQKD.PQALSEHLKNPVIA.KIQKLMDVGLIAIR
Retrocopy IAMHLILEQMQKD>PQALSEHLKNPVIAKKIQKLMDVGLIAIR

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	0.05 RPM	143.43 RPM
SRP007412_cerebellum	0.04 RPM	110.08 RPM
SRP007412_heart	0.00 RPM	38.09 RPM
SRP007412_kidney	0.04 RPM	64.73 RPM
SRP007412_liver	0.00 RPM	31.86 RPM
SRP007412_testis	0.00 RPM	466.82 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_3040 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_3040 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4867
Pan troglodytes	retro_ptro_3242

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015663	2 retrocopies	retro_btau_836, retro_btau_913,
Canis familiaris	ENSCAFG00000014672	6 retrocopies	retro_cfam_1077, retro_cfam_1172, retro_cfam_1722, retro_cfam_1982, retro_cfam_474, retro_cfam_497,
Callithrix jacchus	ENSCJAG00000018209	2 retrocopies	retro_cjac_1043, retro_cjac_2222,
Cavia porcellus	ENSCPOG00000002914	1 retrocopy	retro_cpor_1443,
Felis catus	ENSFCAG00000005937	1 retrocopy	retro_fcat_1510,
Homo sapiens	ENSG00000168439	1 retrocopy	retro_hsap_4867,
Gorilla gorilla	ENSGGOG00000012132	1 retrocopy	retro_ggor_3040 ,
Microcebus murinus	ENSMICG00000016933	1 retrocopy	retro_mmur_1045,
Macaca mulatta	ENSMMUG00000012953	1 retrocopy	retro_mmul_2607,
Nomascus leucogenys	ENSNLEG00000004777	1 retrocopy	retro_nleu_2000,
Pan troglodytes	ENSPTRG00000003820	1 retrocopy	retro_ptro_3242,
Rattus norvegicus	ENSRNOG00000021164	2 retrocopies	retro_rnor_2862, retro_rnor_468,
Ictidomys tridecemlineatus	ENSSTOG00000014262	1 retrocopy	retro_itri_1578,
Tursiops truncatus	ENSTTRG00000010235	1 retrocopy	retro_ttru_1900,