RetrogeneDB ID: retro_pcap_310

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_31200:15237..16110(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBX1
• Ensembl ID: ENSPCAG00000002628
• Aliases: None
• Description: pre-B-cell leukemia homeobox 1 [Source:HGNC Symbol;Acc:8632]

Sequence

>retro_pcap_310
GGTGGGGGCAGCGGGGACGTCCTGGGAGGCCAAGGAAAGCAGCAGATAATAAGCATCACAGACCAGAGCTTCGATGAGGC
CCAGGCCAGAAAACACACCCTCAATTGCCACCCCATGAAGCCTGATCTGTTTAGCATCTTGTGTGAAGTCCAGGAGAAAT
CCAGCCTCAACATCCAAGCTCCCAAGAGCAGGAGCCAATGGACCCGCAACAGATCCGCTTGGACAACATGCTTCTGGCAC
AGGATGTGGCTGGCCTTAAGAAAGGAGGGGACTCAGCAGCAGCTGCTGCAGCAGCCTCTGGGGGTGGAGTATCCCCTGAT
AACTCCATGTAGCACTCTAAACTATCTCAGCAAACTTGCCCAGATGCGCCACATTTTCCACTCAGAGCTGGAAAAGTATG
AGCAGGCATGTAATGAGTTCACAACCCGTGTCATGAATCTGCTGAGGGAGCAGAGTGGTACACGGTCCACGGCAGCCAAG
GGGATGAAGCGCATGGTGAGCGTCTTTCATTGGAAGTTCAGCGCCATCCATATGTGGCTCAAACGGAGCACCTGTGAAGC
TGTCATGATCTTGCATTCAGCTTCCCAGATGCCAGGCGAAAACGTTGGAACTACAGCCAACAGGCTACCGATCCTAAATG
AGTATTTCTACTCCCACCTGAGTAACCCCTATGCTAGCGAGGAGGCTAAAGAGGAGCTTGCCAAGAAGTGTGTCATTACT
GTCTCTCGGGTCTCCCAACTAGTTAGGCAACAGATTTGCTGTAAGAAAAATATTGGAAAATTCCAAGAGGACACAAACAT
CTATGCCGTTAAGACTACTGTGTCAGTCACTCAGGGGGGTCACAGCAGCACCAGTTCCCCGACACCCCCTTCA

Alignment

ORF - retro_pcap_310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.2 %
• Parental protein coverage: 68.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GGRKQDI--GDILQQIMTITDQSLDEAQARKHALNCHRMKPALFNVLCEIKEKTVLSIRG-AQEEEPTDP
          GG...D...G...QQI..ITDQS.DEAQARKH.LNCH.MKP.LF..LCE..EK..L.I....QE.EP.DP
Retrocopy GGGSGDVLGGQGKQQIISITDQSFDEAQARKHTLNCHPMKPDLFSILCEVQEKSSLNIQA<SQEQEPMDP

Parental  QLMRLDNMLLAEGVAGPEKGGGSAAAAAAAAASGGAGSDNSVEHS-DYRAKLSQIRQIYHTELEKYEQAC
          Q..RLDNMLLA..VAG..KGG.SAAAAAAA...GG...DNS..HS..Y..KL.Q.R.I.H.ELEKYEQAC
Retrocopy QQIRLDNMLLAQDVAGLKKGGDSAAAAAAASG-GGVSPDNSM*HS>NYLSKLAQMRHIFHSELEKYEQAC

Parental  NEFTTHVMNLLREQSRTRPISPKEIERMVSIIHRKFSSIQMQLKQSTCEAVMILRS-RFLDARRKRRNFN
          NEFTT.VMNLLREQS.TR....K...RMVS..H.KFS.I.M.LK.STCEAVMIL.S..F.DARRKR.N..
Retrocopy NEFTTRVMNLLREQSGTRSTAAKGMKRMVSVFHWKFSAIHMWLKRSTCEAVMILHS<SFPDARRKRWNYS

Parental  KQATE-ILNEYFYSLSN-YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAV
          .QAT..........LSN.Y.SEEAKEELAKKC.ITVS.VS.......I..KKNIGKFQE..NIYA.KT.V
Retrocopy QQATD>LNEYFYSHLSNPYASEEAKEELAKKCVITVSRVSQ-LVRQQICCKKNIGKFQEDTNIYAVKTTV

Parental  TATNVSAHGSQANSPSTPN
          ..T....H.S...SP..P.
Retrocopy SVTQ-GGH-SSTSSPTPPS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_310 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000001238	1 retrocopy	retro_mdom_1605,
Procavia capensis	ENSPCAG00000002628	1 retrocopy	retro_pcap_310 ,
Sarcophilus harrisii	ENSSHAG00000012750	1 retrocopy	retro_shar_377,
Tarsius syrichta	ENSTSYG00000012332	3 retrocopies	retro_tsyr_1980, retro_tsyr_479, retro_tsyr_723,