RetrogeneDB ID: retro_shar_732

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL861647.1:3460619..3461098(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LGALSL
• Ensembl ID: ENSSHAG00000011885
• Aliases: None
• Description: lectin, galactoside-binding-like [Source:HGNC Symbol;Acc:25012]

Sequence

>retro_shar_732
AAATTAGAGGATGGACATTTGATCAACTCCTTGGGATCTCCTATCCAAACAGATGTGTACTTTCAAAGACTGATGGTATT
ATTTTGTGGGCATGTTTAACATGGGACAAAGCCGGGTAAGAAGATCTTAGTGATGGGGATTGTACACATCAATCCTCAGA
GTTTCCACATCAGTTTGACAAGTGGGAACTCCAAAAACCCTCCTGCAGATGTGGCCATTGAATATTTTCAGTATTTACAG
ATATGTAACTGCTCAGAAATTCATGCATATCAGGAGAAAGAGATGAAGAACAATCAGCAATTCCTTATTTTCCTTTCATC
CCAGACCAACCATTTAGGGTGAAAATTCTCTACGAACATCTATGATTTAGAGTATTTGTGGATGGACACCAGCCTTTTGA
TTTTTATCATTGAATGGAAACACTGTCCTCAATTGACATTATAAAGATCAATGAAGACTTTCAGATCACTACACTTGGC

Alignment

ORF - retro_shar_732 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.64 %
• Parental protein coverage: 92.49 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLEDGHLNNSLGSPVQTDVYFPRLIVPFCGHIKGGMRPGKKILVMGIVDLNPQSFEISLTCGDSKDPPAD
          KLEDGHL.NSLGSP.QTDVYF.RL.V.FCGH...G..PGKKILVMGIV..NPQSF.ISLT.G.SK.PPAD
Retrocopy KLEDGHLINSLGSPIQTDVYFQRLMVLFCGHV*HGTKPGKKILVMGIVHINPQSFHISLTSGNSKNPPAD

Parental  VAIE-LKAIFTDKQLLRNSCIAGERGEEQSAIPYFPFIPDQPFRVEILCEHPRFRVFVDGHQLFDFYHRI
          VAIE.....FTD..LLRNSCI.GER.EEQSAIPYFPFIPDQPFRV.IL.EH..FRVFVDGHQ.FDFYH..
Retrocopy VAIE<IFSVFTDM*LLRNSCISGERDEEQSAIPYFPFIPDQPFRVKILYEHL*FRVFVDGHQPFDFYH*M

Parental  ETLSSIDTIKINGDLQITKLG
          ETLSSID.IKIN.D.QIT.LG
Retrocopy ETLSSIDIIKINEDFQITTLG

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_732 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001067	1 retrocopy	retro_amel_429,
Bos taurus	ENSBTAG00000000156	1 retrocopy	retro_btau_1263,
Dasypus novemcinctus	ENSDNOG00000015222	1 retrocopy	retro_dnov_493,
Felis catus	ENSFCAG00000001209	1 retrocopy	retro_fcat_1280,
Monodelphis domestica	ENSMODG00000003226	2 retrocopies	retro_mdom_1350, retro_mdom_233,
Mus musculus	ENSMUSG00000042363	3 retrocopies	retro_mmus_1637, retro_mmus_272, retro_mmus_2942,
Sarcophilus harrisii	ENSSHAG00000011885	2 retrocopies	retro_shar_315, retro_shar_732 ,