RetrogeneDB ID: retro_ptro_3242

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:86082557..86084186(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STIP1
• Ensembl ID: ENSPTRG00000003820
• Aliases: None
• Description: stress-induced-phosphoprotein 1 [Source:HGNC Symbol;Acc:11387]

Sequence

>retro_ptro_3242
GCTATGAAGCAGGTCAATGAGCTGAAAGAGAAGGGCAACAAGGCCCTGGGCATGGAAAACATCGACAATGCCTTACAGTG
CTACTCCGAAGCCATTAAGCTGGATCCCCACAACCACGTGCTCTACAGCAACTGTTCTGCCACCTATGCCAAGAAAGGAG
ACTACCAGAAGGCTTACAAGGACGGCTGCAAGACCGTCGACCTAAAAGCTTGACTGGGGCAAGGGATATTCACGAAAAGC
AGCAGCTCTAGAGTTCTTAAACCGATTTGAAGAAGCCAAGTGAACCTACGAGGAGAGCTTAAAACACGAGGCAGATAACC
CTCAACTGAAAGAGGGTTTACAGAATATGGAGGCCAGGTTGGCAGAGAGAAAATTTATGAATGCTTTCAACATGCCCAAT
CTGTAACAGAAGTTGGAGAGTGATCCCAGGACAAGGACACTGCTCAGTGATCCTACCTACCGGGAGCTGATAGAGCAACT
ATAAAACAAGCCTTCTGATCTGGGCACAAAACTACAAGATCCCCGGATCCTGACCACTCTCAGTGTCCTCCTTGAGGTCG
ATCGGGGCAGTATGGATGAGGAGGAACAGGTTGCAACACCTTCACCACCACCCCTTCCCAAAAAGGAGACCAAGCCAGAG
CCAGTGGAAGAAGATCTTCCAGAGAATAAGAAGCAGGCACTGAAAGAAAAAGAGCTGAGGAACGATGCCTACAAGAAGAA
AGACTGACAGCCTTGAAGCATTACGACAAAGCCAAGGAGCTGGACCCCAGCAACATGACTTACATTACCAATCAAGCAGC
GGTATACTTTGAAAAGGGCGACTACAATAAGTGCTGGGAGCTTTGTGAGAAGTCCATTGAAGTGGGGAGAGAAAACAGAG
AAGACTATCTACAGATTGCCAAAGTGTGTGCTCGAATTGGCAACTCCTACTTCAAAGAAGAAAAGTACAAGGATGCCATC
CATTTCTATAACAAGTCTCTGGCAGAGCACCGAACTCCAGATGTGCTCAAGAAATGCCAGCAGGCAGAGAAAATCCTGAA
GGAGCAAGAACGGCTGGCCTACATAAACCCCGACCTGGCTTTAGAAGAGAAGAACAAAGGCAACGAGTGTTTTCAGAAAG
GGGACTATCCCCACGCCATGAAGCATTATACGGAAGCCATCAAAAGGAACCCGAAAGATGCCAAATTATACAGCAATCGA
GCTGCCTGTTACACCAAACTCCTGGATTCCAGCTGGCACTCAAGGACTGTGAAGAATGTATCCAGCTAGAACCGACCTTC
ATCAAGGGTTATACACGGAAAGCCGTTGCCCTGGAAGCGATGAAGGACTACACCAAAGTCATGGATGTGTACCGGAAGGC
GCTAGACCCGGACTCCAGCTGTAAGGAGGCGGCAGACGGCTACCAGCGCTGTATGATGGCGCAGTACAACCGGCACCACA
GCCCCGAAGATGTGAAGCAACGAGCCATGGCCGACCCCGAGGTGCAGCAGATCATGAGTGACATAGCCATGCACCTTATC
CTGGAGCAGATGCAGAAGGACCCCCCAGGCACTCAGCGAACACTTAAAGAATCCTGTAATCGCAAAGAAGATCCAGAAGC
TGATGGATTTGGGTCTGATTGCAATTCGA

Alignment

ORF - retro_ptro_3242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.4 %
• Parental protein coverage: 92.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SLRWVNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKP
          ....VNELKEKGNKAL...NID.ALQCYSEAIKLDPHNHVLYSN.SA.YAKKGDYQKAY.DGCKTVDLK.
Retrocopy AMKQVNELKEKGNKALGMENIDNALQCYSEAIKLDPHNHVLYSNCSATYAKKGDYQKAYKDGCKTVDLKA

Parental  -DWGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEARLAERKFMNPFNMPNLYQKLE
          .DWGKGYSRKAAALEFLNRFEEAK.TYEE.LKHEA.NPQLKEGLQNMEARLAERKFMN.FNMPNL.QKLE
Retrocopy >DWGKGYSRKAAALEFLNRFEEAK*TYEESLKHEADNPQLKEGLQNMEARLAERKFMNAFNMPNL*QKLE

Parental  SDPRTRTLLSDPTYRELIEQLRNKPSDLGTKLQDPRIMTTLSVLLGVDLGSMDEEEEIATPPPPPPPKKE
          SDPRTRTLLSDPTYRELIEQL.NKPSDLGTKLQDPRI.TTLSVLL.VD.GSMDEEE..ATP.P.PP..K.
Retrocopy SDPRTRTLLSDPTYRELIEQL*NKPSDLGTKLQDPRILTTLSVLLEVDRGSMDEEEQVATPSP-PPLPKK

Parental  TKPEPMEEDLPENKK-QALKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNK
          .......E......K..A..E..............TALKHYDKAKELDP.NMTYITNQAAVYFEKGDYNK
Retrocopy ETKPEPVEEDLPENK<EAGTERKRAEERCLQEERLTALKHYDKAKELDPSNMTYITNQAAVYFEKGDYNK

Parental  CRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKILK
          C.ELCEK.IEVGRENREDY.QIAK..ARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKILK
Retrocopy CWELCEKSIEVGRENREDYLQIAKVCARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKILK

Parental  EQERLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLE-FQLALKD
          EQERLAYINPDLALEEKNKGNECFQKGDYP.AMKHYTEAIKRNPKDAKLYSNRAACYTKLL..FQLALKD
Retrocopy EQERLAYINPDLALEEKNKGNECFQKGDYPHAMKHYTEAIKRNPKDAKLYSNRAACYTKLLD<FQLALKD

Parental  CEECIQLEPTFIKGYTRKAAALEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQYNRHDSPEDVK
          CEECIQLEPTFIKGYTRKA.ALEAMKDYTK.MDVY.KALD.DSSCKEAADGYQRCMMAQYNRH.SPEDVK
Retrocopy CEECIQLEPTFIKGYTRKAVALEAMKDYTKVMDVYRKALDPDSSCKEAADGYQRCMMAQYNRHHSPEDVK

Parental  RRAMADPEVQQIMSDPAMRLILEQMQKD-PQALSEHLKNPVIAQKIQKLMDVGLIAIR
          .RAMADPEVQQIMSD.AM.LILEQMQKD.PQALSEHLKNPVIA.KIQKLMD.GLIAIR
Retrocopy QRAMADPEVQQIMSDIAMHLILEQMQKD>PQALSEHLKNPVIAKKIQKLMDLGLIAIR

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	115.61 RPM
SRP007412_cerebellum	0.00 RPM	175.44 RPM
SRP007412_heart	0.03 RPM	69.89 RPM
SRP007412_kidney	0.03 RPM	104.45 RPM
SRP007412_liver	0.00 RPM	80.07 RPM
SRP007412_testis	0.32 RPM	413.95 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3242 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3242 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3242 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4867
Gorilla gorilla	retro_ggor_3040

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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,