RetrogeneDB ID: retro_meug_1225

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold332812:203..776(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED4
• Ensembl ID: ENSMEUG00000006810
• Aliases: None
• Description: transmembrane emp24 protein transport domain containing 4 [Source:HGNC Symbol;Acc:22301]

Sequence

>retro_meug_1225
GGACTCATTTCTGCTAGGTGTGTTGTGACAGAACTCATCTGCCTTGCAGGAAATTACTGCATCTAGCTATGAGATAAGCA
GATGGATACTTTCTTCACCCCAGGGCTGGGGATGCATGTGGAAGTGAAGGACCCAGTTGGAAAGCTGGTATTATCATAGC
AATATGATTCAAAAGGTCAATTCACCCGTATCTTCCACACCTCAGATGACAACCAGATCTGCCTATACTCCAATTCTTCT
TGAATGACCATCTTTGTAGGTGGCAAACTAAGGGCACATCTAGACATACAATTCAGCAAGCACACCAACAACTACCCTGA
AACTGTTGCCAAGAATAAATTAATAGAGCTACAGCTCTGTGTTTGCCAGTGACTTGGTCAAATAGAATAGATCCAAAATG
AACAGAACTACCTGCAGTATCATGAGGAATGTTTCTATGTGACCAGCAAGAGCACCAACCAGAGTGTTGTGTTTATTTAG
CACATAAATATTGTTCAGACTGTCATCCTCATCCCCACTACCATCTGGCAGATGCGATACCTTACGGGTTTCCTTGAGGC
AAAAAAGCTGGTG

Alignment

ORF - retro_meug_1225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.2 %
• Parental protein coverage: 85.02 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GETEKRCFIEEIPDETMVIGNYRTQLWDKQTETFLPSTPGLGMHVEVKDPDGKVVLSRQYGSEGRFTFTS
          G....RC...E........GNY...L.DKQ..TF...TPGLGMHVEVKDP.GK.VLS.QY.S.G.FT...
Retrocopy GLISARCVVTEL---ICLAGNYCI*L*DKQMDTFF--TPGLGMHVEVKDPVGKLVLS*QYDSKGQFTRIF

Parental  HTPGDHQICLHSNSTRMTIFAGGKLRVHLDIQVGEHTNNYPEIAAKDKLTELQLRARQLLDQVEQIQKEQ
          HT..D.QICL.SNS..MTIF.GGKLR.HLDIQ...HTNNYPE..AK.KL.ELQL...Q.L.Q.E.IQ.EQ
Retrocopy HTSDDNQICLYSNSS*MTIFVGGKLRAHLDIQFSKHTNNYPETVAKNKLIELQLCVCQ*LGQIE*IQNEQ

Parental  NYQRYREERFRMTSESTNQRVLW---WSIAQTVILILTGIWQMRHLKSFFEAKKLV
          NY..Y.EE.F..TS.STNQ.V.......I.QTVILI.T.IWQMR.L..F.EAKKLV
Retrocopy NYLQYHEECFYVTSKSTNQSVVFI*HINIVQTVILIPTTIWQMRYLTGFLEAKKLV

Legend:

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

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1225 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1225 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007627	2 retrocopies	retro_eeur_12, retro_eeur_317,
Macropus eugenii	ENSMEUG00000006810	1 retrocopy	retro_meug_1225 ,
Monodelphis domestica	ENSMODG00000016129	2 retrocopies	retro_mdom_256, retro_mdom_362,
Oryctolagus cuniculus	ENSOCUG00000003964	1 retrocopy	retro_ocun_1909,
Ictidomys tridecemlineatus	ENSSTOG00000014658	1 retrocopy	retro_itri_1499,