RetrogeneDB ID: retro_amel_868

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192696.1:1424980..1425748(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB4B
• Ensembl ID: ENSAMEG00000016380
• Aliases: None
• Description: None

Sequence

>retro_amel_868
CTGAGGGAGATCTTGCCCCTCCAGGAGAGCCAGTGCAGCAACCAGATCCGCGCCAAATTCGGAGGGTGATCAGCAAGGAG
CGTGGCATTGACCCCACCAGCATTTACCACAGCGACAGCACCCCGAAGCTGGAGCGGATCAACGTGTACTACAAGAAGGT
CACCGGTGGCAAGTACGTACCCTACGCTGAGCTTGTGGACCTGGAGCTGGGCGCTATGACTCCGCGCATTTGGGACCCTT
TGGGCAAATCTTCAGGTCAGACAACTTCGTTTTCGGTCAGAGTTGTGCTGGGAACAGGTGGGCCATGGGGCACTACACAG
AAGGTGAAGAGCCGGTCGACTTGGGGCTGGATGTTGTGAGGAAGGAAGCTGATAGCTGTGACCGCCTGCAGGGCTTCCAG
CTGACCCACTCCCTGGGTAGGGGGACTGAGCCTGGAATGAGTACTCTTCTCATCAGCAAGATCCGGGAGGAGTGCCCAGA
CCGGATCGTGAACACATTCAGTATGGCGCCCTCGCCCAGGGTGTCGGACACAGTGGTGGAGCCCTATGATCCCACCCTCT
TGGTCCACCGGATCGTAGAAAATACAGACGAAACCTATTGCATTGATAACGAGGCCCTCTATGACATCTGCTTTGCAACC
CTAAAACTGACCACGCCCACCTATGGGGACCTCAACCACCTGATGTCAGCCACCATGAGTGGGGTCACACCTGCCAGCGT
TTGCCTGGGCAGCTCAACGCTGACCTGTACAAGCTAGCTGTTAAAATA

Alignment

ORF - retro_amel_868 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.54 %
• Parental protein coverage: 57.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MREIVHLQAGQCGNQIGAKFW-EVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLE
          .REI..LQ..QC.NQI.AKF...VIS.E.GIDPT..YH.DS...LERINVYY...TGGKYVP.A.LVDLE
Retrocopy LREILPLQESQCSNQIRAKFG<RVISKERGIDPTSIYHSDSTPKLERINVYYKKVTGGKYVPYAELVDLE

Parental  PGTM-DSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHS
          .G.M.DS...GPFGQIFR.DNFVFGQS.AGN.WA.GHYTEG.E.VD..LDVVRKEA.SCD.LQGFQLTHS
Retrocopy LGAM<DSAHLGPFGQIFRSDNFVFGQSCAGNRWAMGHYTEGEEPVDLGLDVVRKEADSCDRLQGFQLTHS

Parental  LGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALY
          LG.GT..GM.TLLISKIREE.PDRI.NTFS..PSP.VSDTVVEPY..TL.VH..VENTDETYCIDNEALY
Retrocopy LGRGTEPGMSTLLISKIREECPDRIVNTFSMAPSPRVSDTVVEPYDPTLLVHRIVENTDETYCIDNEALY

Parental  DICFRTLKLTTPTYGDLNHLVSATMSGVT-TCLRFPGQLNADLRKLAVNM
          DICF.TLKLTTPTYGDLNHL.SATMSGVT.TC.R.PGQLNADL.KLAV..
Retrocopy DICFATLKLTTPTYGDLNHLMSATMSGVT<TCQRLPGQLNADLYKLAVKI

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_868 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_868 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016380	2 retrocopies	retro_amel_817, retro_amel_868 ,
Monodelphis domestica	ENSMODG00000017213	1 retrocopy	retro_mdom_117,
Mus musculus	ENSMUSG00000036752	2 retrocopies	retro_mmus_158, retro_mmus_422,