RetrogeneDB ID: retro_shar_19

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841387.1:63966..64911(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000003459
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000017878
• Aliases: None
• Description: None

Sequence

>retro_shar_19
ATGGCTGGTAAGAAGAACGTTCTGTCGTCGCTGGCGGTTTATGCGGAGGATTCGGAGCCCGAATCAGACAGCGAGGCTGG
AGTGGAAGCGGCTGGAAGTGTGATTGCAATAGAGGAAAAAGGCGGCTTAGTGTCTGAAGCCTATGGAGATGATGACTTTT
CTCGACTTGAGGGAGATCAAGATGGCTACGAAGAAGGAGACGAAGAAAACGGCAGGCCATCGGAAGATGGTGATTCAGAG
ACTGAGAAGCCCGAGGCTGATGCCCTAAAGGAGTTTGCAGAACTGGAGAAGAGAGATCCTCAGGAGCTGGTTGCTTCCTT
CTCTGAGAGAGTCAGGAACATGTCTCCTGATGAGATTAAAATTCCCCCAGAGCCACCCGGCAAATGCTCGAATCACCTCC
AGGACAAGATACAGAAGCTATATGAGCGGAAAATAAAGGAAGGGATGGATATGAACTACATCATTCAGAGGAAGAAGGAA
TTTCGGAATCCCAGTATCTATGAGAAGCTTATCCAGTATTGTTCGATTGATGAACTTGGCACCAATTATCCCAAGGATAT
GTTTGATCCTCATGGATGGTCTGAGGACTCTTACTATGAAGCATTAGCTAAAGCACAGAAGATTGAAATGGATAAATTGG
AAAAGGCCAAAAAGGAGAGAACAAAAATTGAGTTTGTGACAGGCACCAAAAAGGGCACCACAAGTAATGCCACAGCCACA
GCAACCACCTCAGCCAACACGGCATCCAGCACCGGGGCTACTGATGCTCAGAAGAGAAAGAGTAAGTGGGATTCTGCTAT
CCCAGTGACCACCATAGCCCAGCCTACAATCCTTACCACAACAACTCCCCTGCCAGCCGTTGTCACAGTGACAACCAGTG
CTAGTGGCTCCAAAACTACTGTCATCTCAGCTGTAGGCACCATTGTGAAGAAAGCCAAGCAATGA

Alignment

ORF - retro_shar_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGKKNVLSSLAVYAEDSEPESDSEAGVEAAGSATAAGLEEKGGLVSEAYGDDDFSRLEGDEDGYEEEDE
          MAGKKNVLSSLAVYAEDSEPESDSEAGVEAAGS..A...EEKGGLVSEAYGDDDFSRLEGD.DGYEE.DE
Retrocopy MAGKKNVLSSLAVYAEDSEPESDSEAGVEAAGSVIA--IEEKGGLVSEAYGDDDFSRLEGDQDGYEEGDE

Parental  ENSRQSEDDDSETEKPETDDLKEFSELEKRDPQELVASFSERVRNMSPDEIKIPPEPPGRCSNHLQDKIQ
          EN.R.SED.DSETEKPE.D.LKEF.ELEKRDPQELVASFSERVRNMSPDEIKIPPEPPG.CSNHLQDKIQ
Retrocopy ENGRPSEDGDSETEKPEADALKEFAELEKRDPQELVASFSERVRNMSPDEIKIPPEPPGKCSNHLQDKIQ

Parental  KLYERKIKEGMDMNYIIQRKKEFRNPSIYEKLIQYCSIDELGTNYPKDMFDPHGWSEDSYYEALAKAQKI
          KLYERKIKEGMDMNYIIQRKKEFRNPSIYEKLIQYCSIDELGTNYPKDMFDPHGWSEDSYYEALAKAQKI
Retrocopy KLYERKIKEGMDMNYIIQRKKEFRNPSIYEKLIQYCSIDELGTNYPKDMFDPHGWSEDSYYEALAKAQKI

Parental  EMDKLEKAKKERTKIEFVTGTKKGTTTNAAATTTTTASTA----ATDAQKRKSKWDSAIPVTTIAQPTIL
          EMDKLEKAKKERTKIEFVTGTKKGTT.NA.AT.TT.A.TA....ATDAQKRKSKWDSAIPVTTIAQPTIL
Retrocopy EMDKLEKAKKERTKIEFVTGTKKGTTSNATATATTSANTASSTGATDAQKRKSKWDSAIPVTTIAQPTIL

Parental  TTTATLPAVVTVTTSASGSKTTVISAVGTIVKKAKQ
          TTT..LPAVVTVTTSASGSKTTVISAVGTIVKKAKQ
Retrocopy TTTTPLPAVVTVTTSASGSKTTVISAVGTIVKKAKQ

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_19 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ficedula albicollis	ENSFALG00000001071	1 retrocopy	retro_falb_23,
Macropus eugenii	ENSMEUG00000013106	2 retrocopies	retro_meug_1388, retro_meug_1734,
Monodelphis domestica	ENSMODG00000007562	4 retrocopies	retro_mdom_1207, retro_mdom_1211, retro_mdom_1212, retro_mdom_1602,
Sarcophilus harrisii	ENSSHAG00000017878	2 retrocopies	retro_shar_19 , retro_shar_47,
Taeniopygia guttata	ENSTGUG00000008426	1 retrocopy	retro_tgut_1,
Tarsius syrichta	ENSTSYG00000009667	2 retrocopies	retro_tsyr_175, retro_tsyr_74,