RetrogeneDB ID: retro_shar_377

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841545.1:2951411..2952025(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBX1
• Ensembl ID: ENSSHAG00000012750
• Aliases: None
• Description: pre-B-cell leukemia homeobox 1 [Source:HGNC Symbol;Acc:8632]

Sequence

>retro_shar_377
GGCTCAGATAACTCAGTTGAGCATTCTGACTCCAGAGGCAAGCTCACAAATCTGATAAACCTATCATACAAAAGTGAAAA
AAAGATGAACAGGCGTGCTGATGAGTTTACCACACATGTGATGAACCTGTTTTGTGAGCAGAGCCAGACCAAGCCCATCT
CACCAAGGGAGAGAATGGTGAGCATCATCCATTGCAAATTTAGCTTCATCCAGATGCAGCCCAAGCAGAATACATGTGAA
GCAGTCATGAGCCTTCATTAGTGATTTTTGGGTGGTAGGTAGAAGAATTGCAACTTCAACAAGCAAGCCACAAATTCCTG
AATAAGTATTTCTATCTCCATCTCAACAAGCCTTACTCTAATGAGGAAGCCAAAAAAAGAGCTAGCCAAGAAATGTGTCA
TCACACTGTTTCACACGTGTTTTAAACTGGTTTGAATAATTGAGTCCAGTATAAAAATAACATAGGTAAATTTCAAGAGG
AAGTCTTTTTCATGCTGCCAAAATGGCTATCACAGTTAGCAATGTTGTCAACCAATAGAAGCCAAACTAACTCTGTCTCA
ACTTGCAATTCATCTAGTTCTTTCAGTTCTTTTAATATGTTAAACTCTGGAGAT

Alignment

ORF - retro_shar_377 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.62 %
• Parental protein coverage: 60.23 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSDNSVEHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVSIIHRKFS
          GSDNSVEHSD.R.KL............K......EFTTHVMNL..EQS.T.PISP.E..RMVSIIH.KFS
Retrocopy GSDNSVEHSDSRGKLTNLINLSYKSEKKMNRRADEFTTHVMNLFCEQSQTKPISPRE--RMVSIIHCKFS

Parental  SIQMQLKQSTCEAVMILRSRFLDARRKRRNFNKQAT-EILNEYFYSHLSNPYPSEEAKEELAKK-CGITV
          .IQMQ.KQ.TCEAVM.L...FL..R.K..NFNKQAT...LN.YFY.HL..PY..EEAK.......C..TV
Retrocopy FIQMQPKQNTCEAVMSLH**FLGGR*KNCNFNKQAT<KFLNKYFYLHLNKPYSNEEAKKRASQEMCHHTV

Parental  SQVSNWFGNKRIRYKKNIGKFQEE-ANIYAAKTAVTATNV-SAHGSQANSPSTPNSAGSSSSFNMSNSGD
          S.V.....N....YK.NIGKFQEE.....AAK.A.T..NV.S...SQ.NS.ST.NS..S.SSFNM.NSGD
Retrocopy SHVF*TGLNN*VQYKNNIGKFQEE<SLFHAAKMAITVSNV>STNRSQTNSVSTCNSSSSFSSFNMLNSGD

Legend:

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

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_377 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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,