RetrogeneDB ID: retro_amel_1684

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193957.1:311101..311632(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C
• Ensembl ID: ENSAMEG00000009175
• Aliases: None
• Description: 5', 3'-nucleotidase, cytosolic [Source:HGNC Symbol;Acc:17144]

Sequence

>retro_amel_1684
CTGCGGGGCTTCTGCTGCAGCCTCCTAGGGGAATTGCACATGGCACTGGAAATGCAACTTGGATTCCCTCGACTGAGAGC
AGTACTGACCTGTGGCTGGACCCAGCAGACAAAGCAGCCAGTGTGTATGAAGCCCAAGGCTTTTTCCTAGACTTGGAGCC
AATCCCTGGAGCCTTGGAAGCCATGCAGGAGATGAGCAACTTGCCAAGACACTGAGGTCTTTAACTGCACCAGCTCTCTG
GTGAAGCATGAATACTGTGTGGGGAGAAGTACTGCTGAATGGAGAATCACCTGGGGCCTCAGTTTGTGGATTGCGATATC
CTGATGAGGGATAGGACCGTTCTTGGGGGACCTGCTCATTGATAACAAGGACACCATGAGAAGCCAAGAGGAGACCCCAA
GCTGGGAGCACATCTTGTTCACCTGCTGCCACAACCAGCATCTGGCCTTGCCCCCCACCCCAAGGAGATGGCTGCTCTCC
TGGAGTGACAGTTGGAGGGAGATCATAGACAGCAAGCAAGGGGCTGGGACA

Alignment

ORF - retro_amel_1684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.78 %
• Parental protein coverage: 99.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LKAFRRRFPGEPHVALEERRGFL-AREQYRALRPDLADKVASVYEAPGFFLDLEPIPGALEAMQEMNNM-
          L..F.....GE.H.ALE...GF....E....L..D.ADK.ASVYEA.GFFLDLEPIPGALEAMQEM.N..
Retrocopy LRGFCCSLLGELHMALEMQLGFP<STESSTDLWLDPADKAASVYEAQGFFLDLEPIPGALEAMQEMSNL>

Parental  QDTEVFICSSPLLNYEHCV-GEKYRWVENHLGPQFVERIILTRDKTVVLG-DLLIDDKDTIRGQEETPSW
          QDTEVF.C.S.L...E.CV.GEKY...ENHLGPQFV...IL.RD.T.VLG.DLLID.KDT.R.QEETPSW
Retrocopy QDTEVFNCTSSLVKHEYCV<GEKYC*MENHLGPQFVDCDILMRDRT-VLG>DLLIDNKDTMRSQEETPSW

Parental  EHILFTCCHNQHLALPPTRRR-LLSWSDNWREIIESKRGART
          EHILFTCCHNQHLALPPT.RR.LLSWSD.WREII.SK.GA.T
Retrocopy EHILFTCCHNQHLALPPTPRRWLLSWSDSWREIIDSKQGAGT

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_1684 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1684 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009175	1 retrocopy	retro_amel_1684 ,
Callithrix jacchus	ENSCJAG00000014578	1 retrocopy	retro_cjac_810,
Felis catus	ENSFCAG00000031408	2 retrocopies	retro_fcat_1016, retro_fcat_606,
Homo sapiens	ENSG00000125458	2 retrocopies	retro_hsap_1441, retro_hsap_1442,
Gorilla gorilla	ENSGGOG00000004740	2 retrocopies	retro_ggor_1061, retro_ggor_1109,
Microcebus murinus	ENSMICG00000017488	1 retrocopy	retro_mmur_1088,
Mustela putorius furo	ENSMPUG00000013985	1 retrocopy	retro_mputfur_1352,
Nomascus leucogenys	ENSNLEG00000000601	2 retrocopies	retro_nleu_1083, retro_nleu_1416,
Pongo abelii	ENSPPYG00000008619	1 retrocopy	retro_pabe_1195,