RetrogeneDB ID: retro_amel_140

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192338.1:4413034..4413489(-)
• Located in intron of: ENSAMEG00000017346

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORMDL2
• Ensembl ID: ENSAMEG00000003047
• Aliases: None
• Description: ORM1-like 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:16037]

Sequence

>retro_amel_140
ATGAATGTGAGGGTGGCACACAGCAAAGTTACCCCCAACACTCAAGTGATGAATAGTCAGGGCATCTGGCTGGCCTATAT
CGTCTTGGTAGGACCGTCACATGTTCTACTCAGCATCCCCTTCTACAGAATACCTGGTATCTGGACCCTGACCAACGTCA
TCCATAACTTGGCTATGTATGTCATCTTCTATACAGTGAAAGGGACACCCTTTGAGACCCCTGACCAAGGAAAGGCTTGG
CTACTGACACACTGGAACAAATGGACTATAGGCTCCAATTTACCTCTTCCTGCAAATTCCTCAGCATTTCTCCCATTGTA
CTCTTCCTCCTGGCCAGCTTCTACACCGAGTATGATGCTGCTCACTTCCTCATCAACACAGCCTCACTGCTCAGCATACT
GCTGCCTAAGTTACCCCAATTCCATGGGGTTCATGTCTTTGGCCTCAACAAATAC

Alignment

ORF - retro_amel_140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.17 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNVGVAHSEVNPNTRVMNSQGTWLAYIILVGLLHAVRLSIRFFSIPVVWTLTNVIHNLAMYVFLHTVKGT
          MNV.VAHS.V.PNT.VMNSQG.WLAYI.LVG..H.V.LSI.F..IP..WTLTNVIHNLAMYV...TVKGT
Retrocopy MNVRVAHSKVTPNTQVMNSQGIWLAYIVLVGPSH-VLLSIPFYRIPGIWTLTNVIHNLAMYVIFYTVKGT

Parental  PFETPDQGKARLLTHW-QQMDYRLQFTSSRKFLSISPIVLYLLASFYTKYDAAHFFINTASLLSVLLPKL
          PFETPDQGKA.LLTHW..QMDYRLQFTSS.KFLSISPIVL.LLASFYT.YDAAHF.INTASLLS.LLPKL
Retrocopy PFETPDQGKAWLLTHW<EQMDYRLQFTSSCKFLSISPIVLFLLASFYTEYDAAHFLINTASLLSILLPKL

Parental  PQFHGVRLFGINKY
          PQFHGV..FG.NKY
Retrocopy PQFHGVHVFGLNKY

Legend:

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

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_140 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_140 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003047	2 retrocopies	retro_amel_140 , retro_amel_735,
Choloepus hoffmanni	ENSCHOG00000009601	1 retrocopy	retro_chof_2232,
Erinaceus europaeus	ENSEEUG00000015224	1 retrocopy	retro_eeur_16,
Felis catus	ENSFCAG00000013964	1 retrocopy	retro_fcat_895,
Macropus eugenii	ENSMEUG00000014896	1 retrocopy	retro_meug_767,
Microcebus murinus	ENSMICG00000010920	1 retrocopy	retro_mmur_212,
Myotis lucifugus	ENSMLUG00000003575	1 retrocopy	retro_mluc_901,
Macaca mulatta	ENSMMUG00000006292	1 retrocopy	retro_mmul_2358,
Mustela putorius furo	ENSMPUG00000000911	2 retrocopies	retro_mputfur_452, retro_mputfur_738,
Mus musculus	ENSMUSG00000025353	1 retrocopy	retro_mmus_2646,
Otolemur garnettii	ENSOGAG00000001695	2 retrocopies	retro_ogar_3016, retro_ogar_951,