RetrogeneDB ID: retro_meug_1627

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold49376:2398..3009(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPH3
• Ensembl ID: ENSMEUG00000013139
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein H3 (2H9) [Source:HGNC Symbol;Acc:5043]

Sequence

>retro_meug_1627
TTGAAGTATACTGCCCCAAATAGCCTTGACAGAGATGACTATGTGTGCTTTAGAGGACTCCCTTTTAGCTGCAACAAGAA
GGGCATTACTCAATTTTTTCAGGTTTGGAAATCATACCAAATGGGATAACATTTCCAGTAGACTTTTGATGGAGGAGTTG
TGGGGAAGCCTTTGTACAGTTTGCTTTCCAGGAAATAGCTGAAAAGGCTCTAAAGAAACACAAGGAAAGAACAGGGCACA
GGTATACTGAAATCTTTAAGAGCAGTCTGACAGAAGTTCATAATCATTATGATCCTGCTCAAGAGCTAATGGCTAGAAAA
CATCCAGGTCCTCATGGTAGACCTCAGGCTGGCAGATGCTATGACAGTCTTAGTAGAGGATCTGGGATTGAAGGAGTGAG
GTGTGGTGCCTGTGAAATTGGGTATACAGGTAATGATGACTATAATGGGTATAGTGATGAATATTACTTTGGAAGAAACC
TCAGTTTCTATTTAGGAATGTCTGGTCATATCTATGGAGACAGCTGGTCTACCTTTCAGAATCCAGCAGGTCATTTTGTG
CACATGAGAGGACTGCCTTACAATGCTATAGAAAATAGAATCTATGATTTT

Alignment

ORF - retro_meug_1627 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.93 %
• Parental protein coverage: 60.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKHNGPNDAASDGTVRLRGLPFGCSKEEIVQFF-TGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAEN
          .K...PN....D..V..RGLPF.C.K..I.QFF..GLEI.PNGIT...D...RS.GEAFVQFA..EIAE.
Retrocopy LKYTAPNSLDRDDYVCFRGLPFSCNKKGITQFF<SGLEIIPNGITFPVDF*WRSCGEAFVQFAFQEIAEK

Parental  ALGKHKERIGHRYIEIFKSSRSEIKGFYDPPRRLLGQR-PGPYDRPLGGRGGYYGAGRGSMYDRMRRGGD
          AL.KHKER.GHRY.EIFKSS..E....YDP...L.....PGP..RP..GR..Y....RGS.....R.G..
Retrocopy ALKKHKERTGHRYTEIFKSSLTEVHNHYDPAQELMARKHPGPHGRPQAGRC-YDSLSRGSGIEGVRCGA-

Parental  GYDGGYGGFDDYGGYNNYGYGNEGFDDR-MRDGRGMGGHGYGGAGDASSGFHG--GHFVHMRGLPFRATE
          ....GY.G.DD...YN..GY..E....R......GM.GH.Y...GD..S.F....GHFVHMRGLP..A.E
Retrocopy -CEIGYTGNDD---YN--GYSDEYYFGRNLSFYLGMSGHIY---GDSWSTFQNPAGHFVHMRGLPYNAIE

Parental  NDIANF
          N.I..F
Retrocopy NRIYDF

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_1627 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1627 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010365	1 retrocopy	retro_acar_184,
Ailuropoda melanoleuca	ENSAMEG00000018064	1 retrocopy	retro_amel_1375,
Bos taurus	ENSBTAG00000014316	2 retrocopies	retro_btau_1504, retro_btau_470,
Callithrix jacchus	ENSCJAG00000019154	2 retrocopies	retro_cjac_292, retro_cjac_578,
Equus caballus	ENSECAG00000007190	1 retrocopy	retro_ecab_912,
Gallus gallus	ENSGALG00000003947	1 retrocopy	retro_ggal_16,
Macropus eugenii	ENSMEUG00000013139	1 retrocopy	retro_meug_1627 ,
Mustela putorius furo	ENSMPUG00000011997	1 retrocopy	retro_mputfur_1469,
Oryctolagus cuniculus	ENSOCUG00000004443	3 retrocopies	retro_ocun_1136, retro_ocun_1379, retro_ocun_1615,
Ictidomys tridecemlineatus	ENSSTOG00000011676	1 retrocopy	retro_itri_647,
Tursiops truncatus	ENSTTRG00000013322	2 retrocopies	retro_ttru_1744, retro_ttru_1766,
Vicugna pacos	ENSVPAG00000011814	1 retrocopy	retro_vpac_403,