RetrogeneDB ID: retro_amel_1270

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193132.1:835180..835804(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OTUB1
• Ensembl ID: ENSAMEG00000018084
• Aliases: None
• Description: OTU domain, ubiquitin aldehyde binding 1 [Source:HGNC Symbol;Acc:23077]

Sequence

>retro_amel_1270
AACAACATCTATTGACAGAAGATCAAGGACCTCCACAAAAAGTACTGGTACATTCGCAAGATCAGGCCTGACTGAAACTG
CTTCTACTGAGCTTTCTGGTTCGCCCACTTGGAGGCACTGCTGGATGACAGCAAGGAATTGCAGCAATTTAAGGCAGTGT
TTGCCAAGAGCAGAGATGACCTGGTTGTCCCAGGGCTTCACCAAGTTCACAGTTGAGGATTTCCACAACATGTTCATGCA
CCTGATACAGCAGGTGGAGAAGTAGACCACTGTAGTGAACCTGCTGGCCTCCTTCAATGACCAGAGCACCTCAGACTACC
AGGTGGTGTACCTGTGGCTGCTCACCTCAGGCTACTGTAGCAGGAAAACAAGTTCTTCCAGCACTTCATGGAGGCAGGTG
GGTGGGGGCTCAAGGAGTTCTTTCAGCAAGAGGTGGAGCCCATGTGCAAGGCAAGTGACCACATTCACATCATTGCACTG
GCCCAGGACCTCAGTGTCTCCATCCAAGTGGAGTATGTGGACCAGGCCAAGGGCAGAACCACCAACCCACACATCTTTCC
CAAGGGCTCCAAACTCAAAGTGTACCTCCTCTATCAGCCTGTACACTAGGATATCCTCTACAAA

Alignment

ORF - retro_amel_1270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.14 %
• Parental protein coverage: 68.77 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DNIYQQKIKDLHKKYSYIRKTRPDGNCFYRAFGFSHLEALLDDSKELQRFKAVSAKSKEDLV-SQGFTEF
          .NIY.QKIKDLHKKY.YIRK.RPD.NCFY.AF.F.HLEALLDDSKELQ.FKAV.AKS..DLV.SQGFT.F
Retrocopy NNIY*QKIKDLHKKYWYIRKIRPD*NCFY*AFWFAHLEALLDDSKELQQFKAVFAKSRDDLV>SQGFTKF

Parental  TIEDFHNTFMDLIEQVEKQTSVADLLASFNDQSTSDYLVVYLRLLTSGYLQR-ESKFFEHFIE-GGRTVK
          T.EDFHN.FM.LI.QVEK.T.V..LLASFNDQSTSDY.VVYL.LLTSGY..R.E.KFF.HF.E.GG...K
Retrocopy TVEDFHNMFMHLIQQVEK*TTVVNLLASFNDQSTSDYQVVYLWLLTSGYCSR<ENKFFQHFMEAGGWGLK

Parental  EFCQQEVEPMCKESDHIHIIALAQALSVSIQVEYMDRGEGGTTNPHIFPEGSEPKVYLLYRPGHYDILYK
          EF.QQEVEPMCK.SDHIHIIALAQ.LSVSIQVEY.D...G.TTNPHIFP.GS..KVYLLY.P.H.DILYK
Retrocopy EFFQQEVEPMCKASDHIHIIALAQDLSVSIQVEYVDQAKGRTTNPHIFPKGSKLKVYLLYQPVH*DILYK

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_1270 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1270 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018084	1 retrocopy	retro_amel_1270 ,
Bos taurus	ENSBTAG00000003967	1 retrocopy	retro_btau_1119,
Canis familiaris	ENSCAFG00000014729	2 retrocopies	retro_cfam_1376, retro_cfam_2023,
Equus caballus	ENSECAG00000002621	1 retrocopy	retro_ecab_760,
Myotis lucifugus	ENSMLUG00000012235	2 retrocopies	retro_mluc_1257, retro_mluc_614,
Mustela putorius furo	ENSMPUG00000013314	1 retrocopy	retro_mputfur_1057,
Pteropus vampyrus	ENSPVAG00000017099	2 retrocopies	retro_pvam_131, retro_pvam_274,
Rattus norvegicus	ENSRNOG00000021175	1 retrocopy	retro_rnor_2431,
Sarcophilus harrisii	ENSSHAG00000004156	1 retrocopy	retro_shar_87,