RetrogeneDB ID: retro_amel_1639

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193820.1:377036..377559(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000004184
• Aliases: None
• Description: None

Sequence

>retro_amel_1639
AAAGTCTTCAAGTGTCTTTTTGGCAAAAAAGAAATGTGCATCCTCATGGTGGGCCTAGATGCTCTGGGGAAGACCACTAC
CTTGTAAAACTGAAGCTGGGTGAGATCGTGACCTCCACTCCCACCATAGGTGTCAGTGTGGAAACCGTGGAGTATACGAA
CATCAGCTTCACCGGGTGGGATGCGGGCGGCCAGGACAAGACCAGCCCTCTGTGACGCCACTGCTCCCAGACCACACAAG
GTCTCATCTTTGTGATTGACAGCAACAACAGAGGGCTTGTGAACTGGACCCATGGGGAGCTCACGAGGATGCTGGTGGTG
GATGAGGTCAGGGATGCGGTCCTCCTGGTGTTGGTGAACAAGCAGGACCTCCCCGAACCATGAATGCCGCCAAGACAACG
GACTAGCTGGGTCTGCACTCCCTGCGCCCCAGGAACTAGTACATTCAGGCCACCTGTGCCACCAGCGGGGCGGAGCTCTA
TGAGCGACTGGACCCGCTGTCCAATCAGCTCCAGAACCAGAAG

Alignment

ORF - retro_amel_1639 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.01 %
• Parental protein coverage: 96.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLFKSLFGKKEMRILMVGLDAAGKTTIL-YKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIR
          K.FK.LFGKKEM.ILMVGLDA.GKTT.L..KLKLGEIVT..PTIG..VETVEY.NISFT.WD.GGQDK..
Retrocopy KVFKCLFGKKEMCILMVGLDALGKTTTL<VKLKLGEIVTSTPTIGVSVETVEYTNISFTGWDAGGQDKTS

Parental  PLWRHYFQNTQGLIFVVDSNDRERVNEAREELTRMLAEDELRDAVLLVFVNKQDL-PNAMNAAEITDKLG
          PL.RH..Q.TQGLIFV.DSN.R..VN....ELTRML..DE.RDAVLLV.VNKQDL.P..MNAA..TD.LG
Retrocopy PL*RHCSQTTQGLIFVIDSNNRGLVNWTHGELTRMLVVDEVRDAVLLVLVNKQDL<PRTMNAAKTTD*LG

Parental  LHSLRQRNWYIQATCATSGDGLYEGLDWLSNQLKTQK
          LHSLR.RN.YIQATCATSG..LYE.LD.LSNQL..QK
Retrocopy LHSLRPRN*YIQATCATSGAELYERLDPLSNQLQNQK

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_1639 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1639 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004184	1 retrocopy	retro_amel_1639 ,
Ailuropoda melanoleuca	ENSAMEG00000007042	2 retrocopies	retro_amel_28, retro_amel_70,
Bos taurus	ENSBTAG00000006785	1 retrocopy	retro_btau_26,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Equus caballus	ENSECAG00000009563	1 retrocopy	retro_ecab_106,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Mus musculus	ENSMUSG00000062421	1 retrocopy	retro_mmus_2056,
Oryctolagus cuniculus	ENSOCUG00000023198	1 retrocopy	retro_ocun_132,
Otolemur garnettii	ENSOGAG00000002503	1 retrocopy	retro_ogar_263,
Ictidomys tridecemlineatus	ENSSTOG00000019768	1 retrocopy	retro_itri_883,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,