RetrogeneDB ID: retro_ptro_2950

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: AACZ03172178.1:1..1261(+)
• 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_2950
GAGCAGGAGTTGAGTGTGCATCCCAAGAGTCTACAAGAAGAGCGCCACCAGTGGACAGCTAGCTTTCTCACCTCAGATTC
TAGGTAGGCAGATAATCACTCCAAGTGAAGGTTATAGATTGTATCCTAGATCCTCCTCTGCTGTTTCAGCTTCATATGAA
ACAACCTTGTCTCAAGAAAGAGATTCTACTATATTTGGTATAAGGGGAAAGAAGTTACATTTTTCATCTTCGTATGCTCA
TAAAGCATCTTCTATTGCCAAATCCTCCAGCTTTTCTTCTATGGAAAGAGAGGAGGAAGACTCTATAATCATCTCCGAAG
GAATAATTGAGGAATACCTAGCATTCGATCACACAGATATGGAAGAGGGATTTCATGGGAAGAAATCAGAAGCAGCTACA
GAGAAACAGAAATTAGGGTATCCTCCCATTGCTCCATTTTACTGCATGAAAGAAGATGTCCTTGTTTATGTGTTTGACAA
TGTATGGAGCAAGGTTGTGAGCTGTATGGAGCAGTTGACACGTAGTCACTGGGAAGGATTTGCCTACCATGATGAGAGTA
ATGTTGCAGTTACCAGACCCGATTCAGAAAGTTTCTGTGTGCTGAGTGAGCCACATCCTTTGGTGTTACCACGAGTGCCA
CAGTCTAAGGTGCTGTCCGTTACCTCAAATCCAATGAGTCTCTGTCAAGCAAGTAGTCATCAGCCAAATGTTAATGGTCT
CTTGGTTCATGGGATGCCTCTACAGCCAAGAAATCTCTCCCTAATGGACAAGCTCCTAGATCTTGATGACAAGCTACTTA
TGAGGCCTGGGACCAGTACCATCCTTTCAACTCGAAATTGGCCAAATCGAGCTGTGGAGGTTTTAGTACATCATCTCTGT
CACACACAGTGCAGTCCACCAAGAGACGCAATCCATCGCCACGAATCCTTCATCCGATAAGCACAAGCCATTCACGTGCT
GGAATACCAAGACTTGTGGAAGAAATCCTCAGAGGAGCCCAAGTCCCAGCGGCAGCCAAATCGCTCTCCTCTCCCTCACC
AATGCCCCTGAGTCGAAATAATCTGCTACCACCTATTGGCACAGCTGAAGTGGAACTTGTGAGCACTGTGGGGCCACAAA
GACAGACAAAGCCCCGTGGCGACTCCAGTCGAGCTCCAAGTGTGGTGGTGGATGAACTTAACTATCAGCAGCCACAAGAA
AGGCTCCTTTTGCCCGACTTTTTCTCCAGGCCCAACACAACTCAATCATTTTTGGTAGAG

Alignment

ORF - retro_ptro_2950 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.03 %
• Parental protein coverage: 72.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EQKLSVHTKSLQEECQQWTASF-PHLR-ILGRQIITPSEGYRLYPRSPSAVSASYETTLSQERDSTIFGI
          EQ.LSVH.KSLQEE..QWTASF..HLR.ILGRQIITPSEGYRLYPRS.SAVSASYETTLSQERDSTIFGI
Retrocopy EQELSVHPKSLQEERHQWTASF<SHLR<ILGRQIITPSEGYRLYPRSSSAVSASYETTLSQERDSTIFGI

Parental  RGKKLHFSSSYAHKASSIAKSSSFCSMERDEEDSIIISEGIIEEYLAFDHIDIEEGFHGKKSEAATEKQK
          RGKKLHFSSSYAHKASSIAKSSSF.SMER.EEDSIIISEGIIEEYLAFDH.D.EEGFHGKKSEAATEKQK
Retrocopy RGKKLHFSSSYAHKASSIAKSSSFSSMEREEEDSIIISEGIIEEYLAFDHTDMEEGFHGKKSEAATEKQK

Parental  LGYPPIAPFYCMKEDVLAYVFDNVWCKVVSCMEQLTRSHWEGFASDDESNVAVTRPDSESSCVLSEPHPL
          LGYPPIAPFYCMKEDVL.YVFDNVW.KVVSCMEQLTRSHWEGFA..DESNVAVTRPDSES.CVLSEPHPL
Retrocopy LGYPPIAPFYCMKEDVLVYVFDNVWSKVVSCMEQLTRSHWEGFAYHDESNVAVTRPDSESFCVLSEPHPL

Parental  VLPRVPQSKVLSITSNPMSLCQASRHQPNVNDLLVHGMPLQPRNLSLMDKLLDLDDKLLMRPGSSTILST
          VLPRVPQSKVLS.TSNPMSLCQAS.HQPNVN.LLVHGMPLQPRNLSLMDKLLDLDDKLLMRPG.STILST
Retrocopy VLPRVPQSKVLSVTSNPMSLCQASSHQPNVNGLLVHGMPLQPRNLSLMDKLLDLDDKLLMRPGTSTILST

Parental  RNWPNRAVEFSTSSLSYTVQS-TRRRNPP-PRTLHPISTSHSCAETPRSVEEILRGARVPVAPNSLSSPS
          RNWPNRAVE.....L..T..S....R..P.PR.LHPISTSHS.A..PR.VEEILRGA.VP.A..SLSSPS
Retrocopy RNWPNRAVEVLVHHLCHTQCS<STKRRNPSPRILHPISTSHSRAGIPRLVEEILRGAQVPAAAKSLSSPS

Parental  PMPLSRNNLLPPIGTAEVEHVSTVGPQRQMKPHGDSSRAQSAVVDEPNYQQPQERLLLPDFFPRPNTTQS
          PMPLSRNNLLPPIGTAEVE.VSTVGPQRQ.KP.GDSSRA.S.VVDE.NYQQPQERLLLPDFF.RPNTTQS
Retrocopy PMPLSRNNLLPPIGTAEVELVSTVGPQRQTKPRGDSSRAPSVVVDELNYQQPQERLLLPDFFSRPNTTQS

Parental  FLLD
          FL..
Retrocopy FLVE

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_2950 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2950 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2950 has 0 orthologous retrocopies within eutheria group .

---

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,