RetrogeneDB ID: retro_amel_817

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192660.1:1408706..1409918(-)
• 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_817
ACTGACCTGCAGCTGGATCGCATCTCCATGTACTACAATGAAGCTACAGGTGGTAAATACGTTCCTCGTGCTATCTTGGT
GGTTCTAGAACCTGGGACCATGGACTCTGTTTGCTCAGGTCCTTTTGGGCAGATATTCAGTCCAGACAACTTTGTTTTTG
GTCAGTCTGGGGCAGGCAACAACTGGGCCAAGAGCCACTATATGGAGGGGGCTGAGCTGGCTGACGCAGTCCTGCATGTG
GTGAGGAAGGAGGCCGAGAGCTGTGACTTCCTGCAGGGTTTCCAACTGACCCACTCACTGGGTGGGGACACAGGCTCTGA
AATGGGCACCTTGCTCATCCACAAGATCCGAGAAGAGTATCCCGACCGCATCATGAACACCTTCAGTGTGGTACCCTCAC
CCAAAGGGTCTGACACTGTGGTTGAACCTTACAATGCCACCCTCTCCGCCCATCAGTTGGTAGAGAACACAGATAAGACC
TACTGCATTGACAACGAGGCCCTTTACGACATCTGCTTCTGCACTCTCAAGCTGACCACACCAACCTACATGGACCTGAA
CCACCTCATCTCAGCCACCATAAACGGTGTCACCACCTGCCTCCACTTCCCTGGTCAGCTCAGTGCTGACCTCCACAAGC
TAGCCATCAACATGGTGCCCTTCCCACGTCTCCACTTCTTCATGCCTGGCTTTGCACCTCTGACCAGCCATGGAAGCCAG
CAGTATCGGGCCCTCACTGTGCCTGAACTCATCCAGCAGGTCTTTGATGCCAAGAACATGATGGCTGCCTGGGACCCCCG
CCATGGCCGTTACCTCACTGTGGCTGTTGTCTTCTGTGGGCGGAAGTCCATGAAGGAGGTAGATGGGCAGATGCTCAACA
TGGAAAACAAGAATAGCAGCTACTTCGTGGAATGGATCCCCAACAACGTCAAGACAGCTGTCTGCAATATCCCACCTTGT
AGCCTCAAGATGGTAGTCACCTTCACTGGAAATAGCACAACCATCCAGGAGCTCTTCAAGCACGTATCAGAGCAGTTCTT
GGCCATGTTCCAGCGCAAGGCCTTCCTCCACCGGTACATAAGTGAGGGCATGGACGAGATGGAGTTCACTGAAGCCAATA
GCAACATGAACGACCTTGTCCCCAAGTACCAGCAGTACTAGGATGCCACCGCAGAAGAAGAGGAGGATTTCGGTGAGGAG
GCTGAAGAGGAG

Alignment

ORF - retro_amel_817 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.9 %
• Parental protein coverage: 90.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDLQLERINVYYNEATGGKYVPRAVLVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEG
          .DLQL.RI..YYNEATGGKYVPRA.LV.LEPGTMDSV.SGPFGQIF.PDNFVFGQSGAGNNWAK.HY.EG
Retrocopy TDLQLDRISMYYNEATGGKYVPRAILVVLEPGTMDSVCSGPFGQIFSPDNFVFGQSGAGNNWAKSHYMEG

Parental  AELVDSVLDVVRKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTV
          AEL.D.VL.VVRKEAESCD.LQGFQLTHSLGG.TGS.MGTLLI.KIREEYPDRIMNTFSVVPSPK.SDTV
Retrocopy AELADAVLHVVRKEAESCDFLQGFQLTHSLGGDTGSEMGTLLIHKIREEYPDRIMNTFSVVPSPKGSDTV

Parental  VEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNAD
          VEPYNATLS.HQLVENTD.TYCIDNEALYDICF.TLKLTTPTY.DLNHL.SAT..GVTTCL.FPGQL.AD
Retrocopy VEPYNATLSAHQLVENTDKTYCIDNEALYDICFCTLKLTTPTYMDLNHLISATINGVTTCLHFPGQLSAD

Parental  LRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRG
          L.KLA.NMVPFPRLHFFMPGFAPLTS.GSQQYRALTVPEL.QQ.FDAKNMMAA.DPRHGRYLTVA.VF.G
Retrocopy LHKLAINMVPFPRLHFFMPGFAPLTSHGSQQYRALTVPELIQQVFDAKNMMAAWDPRHGRYLTVAVVFCG

Parental  -MSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMF
          ..SMKEVD.QMLN..NKNSSYFVEWIPNNVKTAVC.IPP..LKM..TF.GNST.IQELFK..SEQF.AMF
Retrocopy RKSMKEVDGQMLNMENKNSSYFVEWIPNNVKTAVCNIPPCSLKMVVTFTGNSTTIQELFKHVSEQFLAMF

Parental  RRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGEFEEEAEEE
          .RKAFLH.Y..EGMDEMEFTEA.SNMNDLV..YQQY.DATAEEE..F.EEAEEE
Retrocopy QRKAFLHRYISEGMDEMEFTEANSNMNDLVPKYQQY*DATAEEEEDFGEEAEEE

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_817 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_817 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,