RetrogeneDB ID: retro_ptro_1036

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:94213689..94215293(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM149B1
• Ensembl ID: ENSPTRG00000002623
• Aliases: None
• Description: family with sequence similarity 149, member B1 [Source:HGNC Symbol;Acc:29162]

Sequence

>retro_ptro_1036
TCCAGATACACTCGGGAAGGCGATGCCACAGAGCTTGGAGCTGAAAGGAATAACAAAACATGCTCTTAACCATCATCTCC
CTCCCGAGAAGCTGGAGGAAATTTCCCCCACCAGTGACAGTCATGAGAAAGACATAAGTTCCCAAAGCGAGTCTGACATC
ACAAGAGAATCACCTTTTACATCAGCCGATGCTGGGAATTCACTGTCTGCTTTTCCAGGTTATACAGGCGCAGGGATATC
TACTGAAGGCAACTCAGACTTCTCCTGGGAATATGGTGAACTCGATCAAAATGCCACTGAAAAAGCCTGGGCAATGTTCA
CAGCCATTGATGAACTCTTGTATGAGCAGAAGTTGAGTGTGCATACCAAGAGTCTACAAGAAGAGCGCCAACAGTGGACA
GCTAGCTTTCCTCACCTCAGGATTCTAGGTAGGCAGATAATCACTCCAAGTGAAGGTTATAGATTGTATCCTAGATCCTC
CTCTGCTGTTTCAGCTTCATATGAAACAACCTTGTCTCAAGAAAGAGATTCTACTATATTTGGTATAAGGGGAAAGAAGT
TACATTTTTCATCTTCGTATGCTCATAAAGCATCTTCTATTGCCAAATCCTCCAGCTTTTCTTCTATGGAAAGAGAGGAG
GAAGACTCTATAATCATCTCCGAAGGAATAATTGAGGAATACCTAGCATTCGATCACACAGATATGGAAGAGGGATTTCA
TGGGAAGAAATCAGAAGCAGCTACAGAGAAACAGAAATTAGGGTATCCTCCCATTGCTCCATTTTACTGCATGAAAGAAG
ATGTCCTGGTTTATGTGTTTGACAATGTATGGAGCAAGGTTGTGAGCTGTATGGAGCAGTTGACACGTAGTCACTGGGAA
GGATTTGCCTACCATGATGAGAGTAATGTTGCAGTTACCAGACCCGATTCAGAAAGTTTCTGTGTGCTGAGTGAGCCACA
TCCTTTGGTGTTACCACGAGTGCCACAGTCTAAGGTGCTGTCCGTTACCTCAAATCCAATGAGTCTCTGTCAAGAAGTAG
TCATCAGCCAAATGTTAATGGTCTCTTGGTTCATGGGATGCCTCTACAGCCAAGAAATCTCTCCCTAATGGACAAGCTCC
TAGATCTTGATGACAAGCTACTTATGAGGCCTGGGACCAGCACCATCCTTTCAACTCGAAATTGGCCAAATCGAGCTGTG
GAGGTTTTAGTACATCATCTCTGTCACACACAGTGCAGTCCACCAAGAGACGCAATCCATCGCCACGAATCCTTCATCCG
ATAAGCACAAGCCATTCACGTGCTGGAATACCAAGACTTGTGGAAGAAATCCTCAGAGGAGCCCAAGTCCCAGCGGCAGC
CAACTCGCTCTCCTCTCCCTCACCAATGCCCCTGAGTCGAAATAATCTGCTACCACCTATTGGCACAGCTGAAGTGGAAC
TTGTGAGCACTGTGGGGCCACAAAGACAGATGAAGCCCCGTGGCGACTCCAGTCGAGCTCCAAGTGTGGTGGTGGATGAA
CTTAACTATCAGCAGCCACAAGAAAGGCTCCTTTTGCCCGACTTTTTCTCCAGGCCCAACACAACTCAATCATTTTTGGT
AGAG

Alignment

ORF - retro_ptro_1036 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.66 %
• Parental protein coverage: 91.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SRYTR-KAVPQSLELKGITKHALNHHPPPEKLEEISPTSDSHEKDTSSQSKSDITRESSFTSADTGNSLS
          SRYTR.KA.PQSLELKGITKHALNHH.PPEKLEEISPTSDSHEKD.SSQS.SDITRES.FTSAD.GNSLS
Retrocopy SRYTR>KAMPQSLELKGITKHALNHHLPPEKLEEISPTSDSHEKDISSQSESDITRESPFTSADAGNSLS

Parental  AFPSYTGAGISTEGSSDFSWGYGELDQNATEKVQAMFTAIDELLYEQKLSVHTKSLQEECQQWTASFPHL
          AFP.YTGAGISTEG.SDFSW.YGELDQNATEK..AMFTAIDELLYEQKLSVHTKSLQEE.QQWTASFPHL
Retrocopy AFPGYTGAGISTEGNSDFSWEYGELDQNATEKAWAMFTAIDELLYEQKLSVHTKSLQEERQQWTASFPHL

Parental  RILGRQIITPSEGYRLYPRSPSAVSASYETTLSQERDSTIFGIRGKKLHFSSSYAHKASSIAKSSSFCSM
          RILGRQIITPSEGYRLYPRS.SAVSASYETTLSQERDSTIFGIRGKKLHFSSSYAHKASSIAKSSSF.SM
Retrocopy RILGRQIITPSEGYRLYPRSSSAVSASYETTLSQERDSTIFGIRGKKLHFSSSYAHKASSIAKSSSFSSM

Parental  ERDEEDSIIISEGIIEEYLAFDHIDIEEGFHGKKSEAATEKQKLGYPPIAPFYCMKEDVLAYVFDNVWCK
          ER.EEDSIIISEGIIEEYLAFDH.D.EEGFHGKKSEAATEKQKLGYPPIAPFYCMKEDVL.YVFDNVW.K
Retrocopy EREEEDSIIISEGIIEEYLAFDHTDMEEGFHGKKSEAATEKQKLGYPPIAPFYCMKEDVLVYVFDNVWSK

Parental  VVSCMEQLTRSHWEGFASDDESNVAVTRPDSESSCVLSEPHPLVLPRVPQSKVLSITSNPMSLCQ-ASRH
          VVSCMEQLTRSHWEGFA..DESNVAVTRPDSES.CVLSEPHPLVLPRVPQSKVLS.TSNPMSLCQ..S.H
Retrocopy VVSCMEQLTRSHWEGFAYHDESNVAVTRPDSESFCVLSEPHPLVLPRVPQSKVLSVTSNPMSLCQ<RSSH

Parental  QPNVNDLLVHGMPLQPRNLSLMDKLLDLDDKLLMRPGSSTILSTRNWPNRAVEFSTSSLSYTVQS-TRRR
          QPNVN.LLVHGMPLQPRNLSLMDKLLDLDDKLLMRPG.STILSTRNWPNRAVE.....L..T..S....R
Retrocopy QPNVNGLLVHGMPLQPRNLSLMDKLLDLDDKLLMRPGTSTILSTRNWPNRAVEVLVHHLCHTQCS<STKR

Parental  NPP-PRTLHPISTSHSCAETPRSVEEILRGARVPVAPNSLSSPSPMPLSRNNLLPPIGTAEVEHVSTVGP
          ..P.PR.LHPISTSHS.A..PR.VEEILRGA.VP.A.NSLSSPSPMPLSRNNLLPPIGTAEVE.VSTVGP
Retrocopy RNPSPRILHPISTSHSRAGIPRLVEEILRGAQVPAAANSLSSPSPMPLSRNNLLPPIGTAEVELVSTVGP

Parental  QRQMKPHGDSSRAQSAVVDEPNYQQPQERLLLPDFFPRPNTTQSFLLD
          QRQMKP.GDSSRA.S.VVDE.NYQQPQERLLLPDFF.RPNTTQSFL..
Retrocopy QRQMKPRGDSSRAPSVVVDELNYQQPQERLLLPDFFSRPNTTQSFLVE

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	0.00 RPM	17.73 RPM
SRP007412_cerebellum	0.00 RPM	14.23 RPM
SRP007412_heart	0.00 RPM	11.31 RPM
SRP007412_kidney	0.00 RPM	33.08 RPM
SRP007412_liver	0.00 RPM	10.15 RPM
SRP007412_testis	0.63 RPM	52.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1036 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1036 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1036 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1529

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000138286	1 retrocopy	retro_hsap_1529,
Macaca mulatta	ENSMMUG00000011281	1 retrocopy	retro_mmul_2158,
Nomascus leucogenys	ENSNLEG00000016575	1 retrocopy	retro_nleu_1938,
Pan troglodytes	ENSPTRG00000002623	2 retrocopies	retro_ptro_1036 , retro_ptro_2950,
Rattus norvegicus	ENSRNOG00000006554	1 retrocopy	retro_rnor_2124,
Ictidomys tridecemlineatus	ENSSTOG00000002142	1 retrocopy	retro_itri_429,