RetrogeneDB ID: retro_amel_1462

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193422.1:308286..309219(-)
• Located in intron of: ENSAMEG00000003940

Retrocopy information

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

Parental gene information

• Parental gene symbol: UCHL5
• Ensembl ID: ENSAMEG00000015914
• Aliases: None
• Description: None

Sequence

>retro_amel_1462
GACCCCAGGGTCTTCACTGAACTCAAAGGATTTGGTTGCCAAGGAGCCCAAGTAGAAGAAATACGGAGTTTAGAGCCTGA
GAATTTTGAAACGTTAAAGCCAGTTGATGAGTTAATTTTTCTTTTCAAGTGGCAGCCAGGAGAAGAACCAGCAGGCTCTG
TAGTTCAGGACTCCAGACTTGACATATTTTTTGCCAAGCAGGTAATTAATAATGCTTGTGCTACTCAAGCCATAGTAAGT
GTGTTATTGAACTGTACCCATCAAGATGTCATTTAGGAGAGACATTACCAGAGTTTAAAGAATTTTCACAAAGTTTTGAT
GCAGCTATGAAAAGGTTTGGCACTCAGCAGATCAGATGTGATTCGACACGTACACAACAGTTTTGCCAGACAGCAGATGT
TTGAATTTGCTGCAAAGACATCAGCAAAAGAAGAAGATGCTTTTCACTTCGTCAGTTATATTTCTATAAACGGAAGATTG
TATGAATTAGGTGGATTAAGAGAAGGACCGATTGCTTTCCGTGCATGCTATCAGGATGACTGGATCAGCAGTGAGGCCAG
TCATAGAAAAAAAAGATAACCAAAGTACAGTGACAGTGAGATTCAGTTCAACTTAAAGGCCGTTGTGTCTGACAGAAAAA
TGATACATGAAGAGAAGATAGCAGAGTTACAAAGACAACTTGCTGAGGAACCCATGGATACAGATCAGGGTAATAATATG
TTAAATGCTATTCAGTTAGAGGTTACCAAAAATCAGATGCTTATTGAAGAAGAAATACAGAAACTAAAAAGATTTGAAAA
TATCAGAAGGAATCATAATTATCTGCCTTCCATTATGGAATCATTAAAGACTCCAGCAGAACACCAGCAGTTAGCACCAC
GAGTAGAAGAGGCAAAAGGAAAACAGAAGGCAAAGAAAGCACAGGAAACCGAG

Alignment

ORF - retro_amel_1462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.76 %
• Parental protein coverage: 96.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQV
          DP.VFTEL.KGFGC.GAQVEEI.SLEPENFE.LKPV..LIFLFKWQPGEEPAGSVVQDSRLD.IFFAKQV
Retrocopy DPRVFTEL-KGFGCQGAQVEEIRSLEPENFETLKPVDELIFLFKWQPGEEPAGSVVQDSRLD-IFFAKQV

Parental  INNACATQAIVSVLLNCTHQDV-HLGETLSEFKEFSQSFDAAM-KGLALSNSDVIRQVHNSFARQQMFEF
          INNACATQAIVSVLLNCTHQDV.HLGETL.EFKEFSQSFDAAM.KGLALS.SDVIR.VHNSFARQQMFEF
Retrocopy INNACATQAIVSVLLNCTHQDV<HLGETLPEFKEFSQSFDAAM>KGLALSRSDVIRHVHNSFARQQMFEF

Parental  DAKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLM
          .AKTSAKEEDAFHFVSY...NGRLYEL.GLREGPI...AC.QDDWIS...........KYS..EI.FNL.
Retrocopy AAKTSAKEEDAFHFVSYISINGRLYELGGLREGPIAFRACYQDDWISSEASHXXXX*PKYSDSEIQFNLK

Parental  AIVSDRKMIYEQKIAELQRQLAEEEPMDTDQGNNMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHN
          A.VSDRKMI.E.KIAELQRQLA.EEPMDTDQGNNML.AIQ.EV.KNQMLIEEE.QKLKR...ENIRR.HN
Retrocopy AVVSDRKMIHEEKIAELQRQLA-EEPMDTDQGNNMLNAIQLEVTKNQMLIEEEIQKLKRF--ENIRRNHN

Parental  YLPFIMELLKTLAEHQQLIPLVEKAKEKQNAKKAQETK
          YLP.IME.LKT.AEHQQL.P.VE.AK.KQ.AKKAQET.
Retrocopy YLPSIMESLKTPAEHQQLAPRVEEAKGKQKAKKAQETE

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_1462 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1462 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015914	1 retrocopy	retro_amel_1462 ,
Monodelphis domestica	ENSMODG00000012129	1 retrocopy	retro_mdom_1507,
Mustela putorius furo	ENSMPUG00000004619	1 retrocopy	retro_mputfur_259,
Ictidomys tridecemlineatus	ENSSTOG00000000772	1 retrocopy	retro_itri_1814,