RetrogeneDB ID: retro_amel_964

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192773.1:763554..764011(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPAG7
• Ensembl ID: ENSAMEG00000006299
• Aliases: None
• Description: sperm associated antigen 7 [Source:HGNC Symbol;Acc:11216]

Sequence

>retro_amel_964
ATAGAGAGGAACATTCTACACAATATGGTGGAAGTGGCTGGCCTGACATCCTTCTCCTTTGGGAAAAAATGATGAGTGTC
ACGATGTTATGATATTCAAAAAGAAGTTTGCACCCTCAGATGAAAAGCTGGATTCCTACCGTCGTGGGGAGGAGTGGGAC
CTGCAGAAGGTGGAGGAGAAACAGAAGCTGAAGGAGCTGGCCCAGAGGCAGGAGAAGGAAGCAGCCCAGCAGGGGCCCGT
GGTGGTGAGCCCTGCTAGCAACTACAAGGACAAGTATAGCCACCTCATTGGCAAGGGGGAAGCCAAGGATGTGGCCCATA
TGCTACAGGCCAACAAGACCTACAGCTGTGTGCCCATGGCCAACAAGAGGGATCCACGCTCCATTGAAGAGGCCATGAAT
GAGATCCGGGTCAAGAAATGTCTGTGGCAGAGCGGGGAAGAGTTGCCACCTACCTCC

Alignment

ORF - retro_amel_964 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.01 %
• Parental protein coverage: 66.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IERSILHDVVEVAGLTSFSFGE-DDECRYVMIFKKEFAPSDEELDSYRRGEEWDPQKAEEKRKLKELAQQ
          IER.ILH..VEVAGLTSFSFG...DEC..VMIFKK.FAPSDE.LDSYRRGEEWD.QK.EEK.KLKELAQ.
Retrocopy IERNILHNMVEVAGLTSFSFGK>NDECHDVMIFKKKFAPSDEKLDSYRRGEEWDLQKVEEKQKLKELAQR

Parental  QEEAAAQQGPVVVSPASDYKDKYSHLIGKGAAKDAAHMLQANKTYGCVPVANKRDTRSIEEAMNEIRAKK
          QE..AAQQGPVVVSPAS.YKDKYSHLIGKG.AKD.AHMLQANKTY.CVP.ANKRD.RSIEEAMNEIR.KK
Retrocopy QEKEAAQQGPVVVSPASNYKDKYSHLIGKGEAKDVAHMLQANKTYSCVPMANKRDPRSIEEAMNEIRVKK

Parental  RLRQSGEECPPTS
          .L.QSGEE.PPTS
Retrocopy CLWQSGEELPPTS

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_964 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_964 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006299	1 retrocopy	retro_amel_964 ,
Canis familiaris	ENSCAFG00000015761	1 retrocopy	retro_cfam_1417,
Dasypus novemcinctus	ENSDNOG00000011669	1 retrocopy	retro_dnov_1149,
Echinops telfairi	ENSETEG00000020098	1 retrocopy	retro_etel_1489,
Felis catus	ENSFCAG00000030469	1 retrocopy	retro_fcat_833,
Macropus eugenii	ENSMEUG00000007933	1 retrocopy	retro_meug_1358,
Myotis lucifugus	ENSMLUG00000014031	1 retrocopy	retro_mluc_1561,
Mus musculus	ENSMUSG00000018287	1 retrocopy	retro_mmus_2553,
Oryctolagus cuniculus	ENSOCUG00000001108	1 retrocopy	retro_ocun_1103,