RetrogeneDB ID: retro_ptro_2567

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:130861954..130863610(+)
• Located in intron of: ENSPTRG00000019681

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAS2
• Ensembl ID: ENSPTRG00000020544
• Aliases: None
• Description: None

Sequence

>retro_ptro_2567
ATGCATTGTGAGAGGTTTCTATGTATCCTGAGAATAATTGGAACCACACTCTTTGGAGTCTCTCTCCTCCTTGGAATCAC
AGCTGCTTATATTGTTGGCTACCAGTTTATCCAAACGGATAATTACTATTTCTCTTTTGGACTGTATGGTGCCTTTTTGG
CATCACACCTCATCATCCAAAGCCTGTTTGCCTTTTTGGAGCACCAAAAAATGAAAAAATCCCTAGAAACCCCCATAAAG
TTGAACAAAACAGTTGCCCTTTGCATCGCTGCCTATCAAGAAGATCCAGACTACTTAAGGAAATGTTTGCAATCTGTGAA
AAGGCTAACCTACCCTGGGATTAAAGTTGTCATGGTCATAGATGGGAACTCAGAAGATGACCTTTACATGATGGACATCT
TCAGTGAAGTCATGGGCAGAGACAAATCAGCCACTTATATCTGGAAGAACAACTTCCACGAAAAGGGTCCCGGTGAGACA
GATGAGTCACATAAAGAAAGCTCGCAACATGTAACGCAATTGGTCTTGTCCAACAAAAGTATCTGCATCATGCAAAAATG
GGGTGGAAAAAGAGAAGTCATGTACACAGCCTTCAGAGCACTGGGACGAAGTGTGGATTATGTACAGGTTTGTGATTCAG
ACACTATGCTTGACCCAGCCTCATCTGTGGAGATGGTAAAAGTTTTAGAAGAAGATCCCATGGTTGGAGGTGTTGGGGGA
GATGTCCAGATTTTAAACAAGTACGATTCCTGGATCTCATTCCTCAGCAGTGTAAGATATTGGATGGCTTTTAATATAGA
AAGGGCCTGTCAGTCTTATTTTGGGTGTGTTCAGTGCATTAGTGGACCTCTGGGAATGTACAGAAACTCCTTGTTGCATG
AGTTTGTGGAAGATTGGTACAATCAAGAATTTATGGGCAACCAATGTAGCTTTGGTGATGACAGGCATCTCACGAACCGG
GTGCTGAGTCTGGGCTATGCAACAAAATACACAGCTCGATCTAAGTGCCTTACTGAAACACCTATAGAATATCTCAGATG
GCTAAACCAGCAGACCCGTTGGAGCAAGTCCTACTTCCGAGAATGGCTGTACAATGCAATGTGGTTTCACAAACATCACT
TGTGGATGACCTACGAAGCGATTATCACTGGATTCTTTCCTTTCTTTCTCATTGCCACAGTAATCCAGCTCCTCTACCGG
GGTAAAATTTGGAACATTCTCCTCTTCTTGTTAACTGTCCAGCTAGTAGGTCTCATAAAATCATCTTTTGCCAGCTGCCT
TAGAGGAAATATCGTCATGGTCTTCATGTCTCTCTACTCAGTGTTATACATGTCAAGTTTACTTCCCGCCAAGATGTTTG
CAATTGCAACAATAAACAAAGCTGGGTGGGGCACATCAGGAAGGAAAACCATTGTTGTTAATTTCATAGGACTCATTCCA
GTATCAGTTTGGTTTACAATTCTCCTGGGTGGTGTGATTTTCACCATTTATAAGGAGTCTAAAAGGCCATTTTCAGAATC
CAAACAGACAGTTCTAATTGTTGGAACGTTGCTCTATGCATGCTATTGGGTCATGCTTTTGACGCTGTATGTAGTTCTCA
TCAATAAGTGTGGCAGGCGGAAGAAGGGACAACAATATGACATGGTGCTTGATGTA

Alignment

ORF - retro_ptro_2567 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHCERFLCILRIIGTTLFGVSLLLGITAAYIVGYQFIQTDNYYFSFGLYGAFLASHLIIQSLFAFLEHRK
          MHCERFLCILRIIGTTLFGVSLLLGITAAYIVGYQFIQTDNYYFSFGLYGAFLASHLIIQSLFAFLEH..
Retrocopy MHCERFLCILRIIGTTLFGVSLLLGITAAYIVGYQFIQTDNYYFSFGLYGAFLASHLIIQSLFAFLEHXX

Parental  MKKSLETPIKLNKTVALCIAAYQEDPDYLRKCLQSVKRLTYPGIKVVMVIDGNSEDDLYMMDIFSEVMGR
          ...SLETPIKLNKTVALCIAAYQEDPDYLRKCLQSVKRLTYPGIKVVMVIDGNSEDDLYMMDIFSEVMGR
Retrocopy XXXSLETPIKLNKTVALCIAAYQEDPDYLRKCLQSVKRLTYPGIKVVMVIDGNSEDDLYMMDIFSEVMGR

Parental  DKSATYIWKNNFHEKGPGETDESHKESSQHVTQLVLSNKSICIMQKWGGKREVMYTAFRALGRSVDYVQV
          DKSATYIWKNNFHEKGPGETDESHKESSQHVTQLVLSNKSICIMQKWGGKREVMYTAFRALGRSVDYVQV
Retrocopy DKSATYIWKNNFHEKGPGETDESHKESSQHVTQLVLSNKSICIMQKWGGKREVMYTAFRALGRSVDYVQV

Parental  CDSDTMLDPASSVEMVKVLEEDPMVGGVGGDVQILNKYDSWISFLSSVRYWMAFNIERACQSYFGCVQCI
          CDSDTMLDPASSVEMVKVLEEDPMVGGVGGDVQILNKYDSWISFLSSVRYWMAFNIERACQSYFGCVQCI
Retrocopy CDSDTMLDPASSVEMVKVLEEDPMVGGVGGDVQILNKYDSWISFLSSVRYWMAFNIERACQSYFGCVQCI

Parental  SGPLGMYRNSLLHEFVEDWYNQEFMGNQCSFGDDRHLTNRVLSLGYATKYTARSKCLTETPIEYLRWLNQ
          SGPLGMYRNSLLHEFVEDWYNQEFMGNQCSFGDDRHLTNRVLSLGYATKYTARSKCLTETPIEYLRWLNQ
Retrocopy SGPLGMYRNSLLHEFVEDWYNQEFMGNQCSFGDDRHLTNRVLSLGYATKYTARSKCLTETPIEYLRWLNQ

Parental  QTRWSKSYFREWLYNAMWFHKHHLWMTYEAIITGFFPFFLIATVIQLFYRGKIWNILLFLLTVQLVGLIK
          QTRWSKSYFREWLYNAMWFHKHHLWMTYEAIITGFFPFFLIATVIQL.YRGKIWNILLFLLTVQLVGLIK
Retrocopy QTRWSKSYFREWLYNAMWFHKHHLWMTYEAIITGFFPFFLIATVIQLLYRGKIWNILLFLLTVQLVGLIK

Parental  SSFASCLRGNIVMVFMSLYSVLYMSSLLPAKMFAIATINKAGWGTSGRKTIVVNFIGLIPVSVWFTILLG
          SSFASCLRGNIVMVFMSLYSVLYMSSLLPAKMFAIATINKAGWGTSGRKTIVVNFIGLIPVSVWFTILLG
Retrocopy SSFASCLRGNIVMVFMSLYSVLYMSSLLPAKMFAIATINKAGWGTSGRKTIVVNFIGLIPVSVWFTILLG

Parental  GVIFTIYKESKRPFSESKQTVLIVGTLLYACYWVMLLTLYVVLINKCGRRKKGQQYDMVLDV
          GVIFTIYKESKRPFSESKQTVLIVGTLLYACYWVMLLTLYVVLINKCGRRKKGQQYDMVLDV
Retrocopy GVIFTIYKESKRPFSESKQTVLIVGTLLYACYWVMLLTLYVVLINKCGRRKKGQQYDMVLDV

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	0.04 RPM	0.30 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.29 RPM
SRP007412_kidney	0.00 RPM	0.05 RPM
SRP007412_liver	0.00 RPM	0.23 RPM
SRP007412_testis	0.11 RPM	4.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2567 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2567 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2567 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000020544	1 retrocopy	retro_ptro_2567 ,