RetrogeneDB ID: retro_shar_779

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL864789.1:185793..186253(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZFAND2A
• Ensembl ID: ENSSHAG00000000364
• Aliases: None
• Description: zinc finger, AN1-type domain 2A [Source:HGNC Symbol;Acc:28073]

Sequence

>retro_shar_779
CTGGATTATCTTCCATTAAACTGTGCCGCATGTAACAAAGTCTTTTGTAAAGCTCATGTTCAATTGGAGCAGCATAAATG
CAGTGCTTCATATAAAAAGGATGTTCGGGTCCCAGTATGTCCAGTTTGTCATGTCCCTGTTCCAGTAAGACGGGGAGAAA
CCGCAGATGTTGTGATTGGACAGCATATGGATAAAGACTGTAAATATAACCCGGCTCGGGAGAAAAAGATTTTCGTACAC
CGGTGCTCAAAGGAGGGGTGCAAGAAGAAAGAAATGTTTGAGCTGCTTTGTGACCAGTGTAATGACAACTTCTGTATTAA
GCACAGGCATCCTTTGGATCATAACTGCAAACATTGACCATCCCATCTCCAGAGGAGGGTGTGCAGCTATAATGAGAGCT
TCTGAATCATCTGGCGCTTCAAACAAATTATCTTCCAGTTGGCTAGCTCAGTGATTAAGA

Alignment

ORF - retro_shar_779 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.23 %
• Parental protein coverage: 97.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LDYLPLNCAACNKVFCKAHVQLEQHKCSASYKKDVRVPVCPLCHVPVPVGRGETADVVVGQHMDKDCKYN
          LDYLPLNCAACNKVFCKAHVQLEQHKCSASYKKDVRVPVCP.CHVPVPV.RGETADVV.GQHMDKDCKYN
Retrocopy LDYLPLNCAACNKVFCKAHVQLEQHKCSASYKKDVRVPVCPVCHVPVPVRRGETADVVIGQHMDKDCKYN

Parental  PAGEKKIFVHRCSKEGCKKKEMFELLCDQCNDNFCIKHRHPLDHNCKHIDHPISRGGC-AAIMRASESSG
          PA.EKKIFVHRCSKEGCKKKEMFELLCDQCNDNFCIKHRHPLDHNCKH......R..C.A.......S..
Retrocopy PAREKKIFVHRCSKEGCKKKEMFELLCDQCNDNFCIKHRHPLDHNCKH*PSHLQRRVC>AIMRASESSGA

Parental  ASNKLSSSWLAQRLR
          ...KLSSSWLAQ.LR
Retrocopy SN-KLSSSWLAQ*LR

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_779 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015776	1 retrocopy	retro_cjac_2957,
Loxodonta africana	ENSLAFG00000005496	1 retrocopy	retro_lafr_211,
Microcebus murinus	ENSMICG00000002112	1 retrocopy	retro_mmur_441,
Monodelphis domestica	ENSMODG00000025494	1 retrocopy	retro_mdom_34,
Sarcophilus harrisii	ENSSHAG00000000364	2 retrocopies	retro_shar_756, retro_shar_779 ,
Tupaia belangeri	ENSTBEG00000007079	2 retrocopies	retro_tbel_2636, retro_tbel_2697,