RetrogeneDB ID: retro_meug_1971

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold75791:2171..2719(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPDL
• Ensembl ID: ENSMEUG00000011454
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D-like [Source:HGNC Symbol;Acc:5037]

Sequence

>retro_meug_1971
GAGTTTTTTGACAGACCTAAAATCAGTAGTATCAAGAATCACCAGGATGATGGTAAGATGCTTATTACAGGGCTAAGTTG
GGATACAAATAAAAAAGAACCAATTAATTACATAGAATTTTTTAAAAGAAGTTGTATGCTGCACAATTGAAACAGATATA
GTCATTGGAAGACGAAGGGGATTTGGATTTATGCTTTCTTAAGATTGTGTTAAGGTCCTGGAACTTAAAGACTACAGACT
AGATGGCAAGTTGATAGACTCCCCCAAGTCTAAAATTTTAAAGGAAAAGATCCTCCCTAAAGTATTTTTTGGGTAAACTG
AGTCCAGATACATCTGAAGAACCAATCAGAGAATACTTGGGGACATTTGGAGGGATTCAGCCTATTTAACTTCCTATAGA
CACAAAAACAAATGAAAGAAGAGGATTCTGTATCATCACATATACAAATGAAGAACTAGTAAGGAAATTATTAGAAAACA
TATACCATAAAAGTGATTTTGAGATATGTAGAATCAAAGTTGCACATGCCAAAGCAGTATGCAGGCAA

Alignment

ORF - retro_meug_1971 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.38 %
• Parental protein coverage: 76.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EFAEGSKINASKNQQDDGKMFIGGLSWDTSKKDLTEYLSRFG-EVVDCTIKTDPVTGRSRGFGFVLFKDA
          EF....KI...KN.QDDGKM.I.GLSWDT.KK....Y...F..EVV.CTI.TD.V.GR.RGFGF.L..D.
Retrocopy EFFDRPKISSIKNHQDDGKMLITGLSWDTNKKEPINYIEFFK>EVVCCTIETDIVIGRRRGFGFMLS*DC

Parental  ASVDKVLELKEHKLDGKLIDPKRAKALK-GKEPP-KKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMD
          ....KVLELK...LDGKLID....K.LK.GK.PP..K.F.G.LSPDTSEE.I.EY.G.FG.I..I.LP.D
Retrocopy V---KVLELKDYRLDGKLIDSPKSKILK<GKDPP<LKYFLGKLSPDTSEEPIREYLGTFGGIQPI*LPID

Parental  TKTNERRGFCFITYTDEEPVKKLLENRYHQIGSGKCEIKVAQPKEVYRQ
          TKTNERRGFC.ITYT.EE.V.KLLEN.YH......C.IKVA..K.V.RQ
Retrocopy TKTNERRGFCIITYTNEELVRKLLENIYHKSDFEICRIKVAHAKAVCRQ

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_1971 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1971 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 11 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015197	1 retrocopy	retro_cjac_2589,
Dasypus novemcinctus	ENSDNOG00000003887	7 retrocopies	retro_dnov_1175, retro_dnov_1182, retro_dnov_144, retro_dnov_1603, retro_dnov_31, retro_dnov_723, retro_dnov_930,
Felis catus	ENSFCAG00000000455	1 retrocopy	retro_fcat_1568,
Macropus eugenii	ENSMEUG00000001084	2 retrocopies	retro_meug_1897, retro_meug_214,
Macropus eugenii	ENSMEUG00000007909	2 retrocopies	retro_meug_169, retro_meug_246,
Macropus eugenii	ENSMEUG00000011454	7 retrocopies	retro_meug_1252, retro_meug_1378, retro_meug_1491, retro_meug_1971 , retro_meug_2165, retro_meug_249, retro_meug_766,
Macropus eugenii	ENSMEUG00000013622	6 retrocopies	retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Monodelphis domestica	ENSMODG00000011916	6 retrocopies	retro_mdom_1496, retro_mdom_1789, retro_mdom_1951, retro_mdom_2017, retro_mdom_546, retro_mdom_981,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Ictidomys tridecemlineatus	ENSSTOG00000013979	1 retrocopy	retro_itri_1177,
Tursiops truncatus	ENSTTRG00000001793	2 retrocopies	retro_ttru_1486, retro_ttru_744,