RetrogeneDB ID: retro_meug_1813

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold61268:8853..9532(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED8
• Ensembl ID: ENSMEUG00000013567
• Aliases: None
• Description: mediator complex subunit 8 [Source:HGNC Symbol;Acc:19971]

Sequence

>retro_meug_1813
CCTTCAGTCCTGGATAGCTTTGCTCTGTTCTCTGGATAGTTGAACACCTTCAACAAGGTCCTCAAACACAAGAAGACCCC
ATTGCTCCGGAACCAAGTTATCATTCCTCTGGTGCTGTCCCCAGACCAAGATGAGGAGCTCATGTGCTAGACAGAGGGCG
GGATTTCTGTCTTCAGTCATGAGGTGATCTCTGACCACCTAAGAACCAAACCAGACCCAGAGTGGAGCAGCAGGAGAAGC
AACTGACCACAGACGCTGCTCGAATCTGCACCAATGCTGCCCAGAAGCAAATACAGACCTTAAATAAAATGTGCTCAAAC
CTACTGGAAAAAATCAGCAAAGAGGAATGAGAGTCAGAAAGTGGAGGTCTCCATTAAAATAAACAGACCTTCAACCTCAC
AGACACCAATACCCTGGTGGATGCAGTTGCATTTGGTAAGGGTCTGTCTAACTGGAGACCTCCTGGCACCAGTGGCCCCG
GGCCAAGCAGGCCCAGCCTGGGGCAGGAACCCTCCTGGCTGGAGCTTCTGGCATGCAGCATGTTCATATGACAGGTGCAT
CCAGTCAGCAACAGAGCACTCTGCTCAGTGGAGTACAGATGGCGCAAACTGGTCAGCCAGGTAAGATGCCAAGCGTCATC
AAAACCAACATCAAGTCAGCTTCCATGCACCCCTACCAG

Alignment

ORF - retro_meug_1813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.59 %
• Parental protein coverage: 84.96 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PSVLDSFALLSGQLNTLNKVLKHEKTPLLRNQVIIPLVLSPDRDEELTRQTEGRVPVFSHEVVPDHLRTK
          PSVLDSFAL.SG.LNT.NKVLKH.KTPLLRNQVIIPLVLSPD.DEEL...TEG...VFSHEV..DHLRTK
Retrocopy PSVLDSFALFSG*LNTFNKVLKHKKTPLLRNQVIIPLVLSPDQDEELMC*TEGGISVFSHEVISDHLRTK

Parental  PDPE-VEEQEKQLTTDAARIGTDAAQKQIQTLNKMCSNLLEKISKEERESESGGLRQNKQTFNPTDTNAL
          PDPE.VE.QEKQLTTDAARI.T.AAQKQIQTLNKMCSNLLEKISKEE.ESESGGL..NKQTFN.TDTN.L
Retrocopy PDPE<VEQQEKQLTTDAARICTNAAQKQIQTLNKMCSNLLEKISKEE*ESESGGLH*NKQTFNLTDTNTL

Parental  VAAVAFGKGLSNWRSPGTSG-PGQAG-QSGAGTLLTGASGMQQVQMTGTSSQQQSTLLSGVQMAQAGQPG
          V.AVAFGKGLSNWR.PGTSG.PGQAG.Q.GAGTLL.GASGMQ.V.MTG.SSQQQSTLLSGVQMAQ.GQPG
Retrocopy VDAVAFGKGLSNWRPPGTSG>PGQAG>QPGAGTLLAGASGMQHVHMTGASSQQQSTLLSGVQMAQTGQPG

Parental  KMPSGIKTNIKSASMHPYQ
          KMPS.IKTNIKSASMHPYQ
Retrocopy KMPSVIKTNIKSASMHPYQ

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_1813 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1813 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005237	1 retrocopy	retro_cfam_458,
Erinaceus europaeus	ENSEEUG00000002286	1 retrocopy	retro_eeur_117,
Macropus eugenii	ENSMEUG00000013567	1 retrocopy	retro_meug_1813 ,
Myotis lucifugus	ENSMLUG00000012621	1 retrocopy	retro_mluc_1618,
Monodelphis domestica	ENSMODG00000011310	1 retrocopy	retro_mdom_1131,
Oryctolagus cuniculus	ENSOCUG00000027895	2 retrocopies	retro_ocun_1088, retro_ocun_67,
Otolemur garnettii	ENSOGAG00000001865	1 retrocopy	retro_ogar_2091,
Ictidomys tridecemlineatus	ENSSTOG00000009737	1 retrocopy	retro_itri_818,