RetrogeneDB ID: retro_amel_1368

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193267.1:123085..123979(+)
• Located in intron of: ENSAMEG00000005956

Retrocopy information

• Ensembl ID: ENSAMEG00000020299
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HSDL2
• Ensembl ID: ENSAMEG00000006832
• Aliases: None
• Description: None

Sequence

>retro_amel_1368
ATGATGAATGTCAACACCAGAGGCACGTTTCTGACATCTAAAGCATGTATTCCTTATTTGAAAAAGAGTAAAATTGCTCA
TATACTCAATCTCAGTCCACCGCTGAACCTAAATCCATTGTGGTTCAAGCAGCACTGTGCTTAGACCATTGCTAAGTATG
GAATGTCTATGTGTGTGCTTGGAATGGCAGAAGAATTTAAGGGTGAAACCGCAGTCAATGCATTATGGCCTAAAACAGCC
ATCCACACCGCTGCTATGGATATGCTGGGAGGATCCAGCATTGAAAGCCAGTGTAGAAAAGTTGGTATCATTGCGGATGC
TGCCTATTCCGTTTTTAAAAAGCCAAAAATTTTTCCTGGAAACTTTATAATTGATGAAAATATCTTAAGAGAAGAAGGAA
TAAAAAATTTTGACATCTATGCAATTAAACCAGGCCATCCTTTGTTACCAGATTTCTTCTTAGATGAACACCCAGATACA
ATTACCAAGAAAATGGAATCACATGATGCTGTTCCAGAGTTGAAAGAAGAGAAGTCACAGCCACCACCAAAACCACGTTC
TGGAGCTGTGGCAGAAACATTTAGAATTGTTAAGGACCCTCTCAGTGATGACATTGTGAAAGCCACTCAAGCAATTTATC
AGTTTGAACTCTCAGGCGAAGATGATGGAACATGGTTTCTTGATCTTAAAACCAAAGGCGGGAACGTCGGCTATGGAGAG
CCCTCTGATCAGGCAGATGTGGTGATGAGTATGTCTACTGGTGATTTTGTAAAAATGTTTTCAGGGAAACTAAAACCAAC
AATGGCATTCATGTCGGGAAAATTGAAGATTAAAGGAAACATGACCCTAGCAATCCGATTGGAGAAGCTAATGAATCAGA
TGAATGCCAGGCTG

Alignment

ORF - retro_amel_1368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.97 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMNVNTRGTFLTSKACIPYLKKSKIAHILNLSPPLNLNPLWFKQHCAYTIAKYGMSMCVLGMAEEFKGET
          MMNVNTRGTFLTSKACIPYLKKSKIAHILNLSPPLNLNPLWFKQHCA.TIAKYGMSMCVLGMAEEFKGET
Retrocopy MMNVNTRGTFLTSKACIPYLKKSKIAHILNLSPPLNLNPLWFKQHCA*TIAKYGMSMCVLGMAEEFKGET

Parental  AVNALWPKTAIHTAAMDMLGGSGIESQCRKVDIIADAAYSIFKKPKTFTGNFIIDENILREEGIKNFDIY
          AVNALWPKTAIHTAAMDMLGGS.IESQCRKV.IIADAAYS.FKKPK.F.GNFIIDENILREEGIKNFDIY
Retrocopy AVNALWPKTAIHTAAMDMLGGSSIESQCRKVGIIADAAYSVFKKPKIFPGNFIIDENILREEGIKNFDIY

Parental  AIKPGHPLLPDFFLDEHPDTITKKMESHDAVPELKEKKSQPPPKPRSGAVAETFRIVKDSLSDDVVKATQ
          AIKPGHPLLPDFFLDEHPDTITKKMESHDAVPELKE.KSQPPPKPRSGAVAETFRIVKD.LSDD.VKATQ
Retrocopy AIKPGHPLLPDFFLDEHPDTITKKMESHDAVPELKEEKSQPPPKPRSGAVAETFRIVKDPLSDDIVKATQ

Parental  AIYQFELSGEDGGTWFLDLKSKGGNVGYGEPSDQADVVMSMSTEDFVKMFSGKLKPTMAFMSGKLKIKGN
          AIYQFELSGED.GTWFLDLK.KGGNVGYGEPSDQADVVMSMST.DFVKMFSGKLKPTMAFMSGKLKIKGN
Retrocopy AIYQFELSGEDDGTWFLDLKTKGGNVGYGEPSDQADVVMSMSTGDFVKMFSGKLKPTMAFMSGKLKIKGN

Parental  MTLAIRLEKLMNQMNARL
          MTLAIRLEKLMNQMNARL
Retrocopy MTLAIRLEKLMNQMNARL

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_1368 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1368 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006832	1 retrocopy	retro_amel_1368 ,
Canis familiaris	ENSCAFG00000003028	1 retrocopy	retro_cfam_480,
Nomascus leucogenys	ENSNLEG00000016534	1 retrocopy	retro_nleu_649,
Ictidomys tridecemlineatus	ENSSTOG00000012222	1 retrocopy	retro_itri_471,
Tupaia belangeri	ENSTBEG00000013420	2 retrocopies	retro_tbel_2324, retro_tbel_3321,