RetrogeneDB ID: retro_amel_336

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192390.1:2576253..2576923(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GHITM
• Ensembl ID: ENSAMEG00000009753
• Aliases: None
• Description: growth hormone inducible transmembrane protein [Source:HGNC Symbol;Acc:17281]

Sequence

>retro_amel_336
ACCCATCAGAGAACTGGTATCTGGTGTGGAAAAGCTGGCCAAGAACCCAAGGAGGCAGTATTGGAACCATCGATAGAAAA
ATATTTAAATTTGATCAGATGAGAAGATGGCTTATTGCTGGACGGCCTGCTTGGTCTTGGAGCATTGTTCTACTATGGCT
TAGGAATATATAATGAAATTGTAACCATTGAAAAGGCTGTAATTTGGCCTCGGTATGTTAAGAACAGAAATCATTCTATG
CATATATACTTAGCAGGAAGTATTGGTTTTACAGCTTTGTCCACCCTGGAAGTAAACAGAACTCTTCTCATGAACATGAT
CAGAGGCTCTTGGGTGAGAACTGGTGCAACCTTTGAAGCCATATTGGAGGTGGAATGCTGGTACAATCAATATTATATGA
CCAGAGCCCAAGACCCTAAGGAACTTGCTTAGTTATTCTACTCTAGTGTGAAGGGTCCCATAATGGCTCCTCTCACGATG
GGGGGGGGGGCCTCTCCTCATCAGAGCTGCATAGTACACAGTGGGCCTCGGAAGAGGCCCCTCCACTTTGGCCACGTGTG
CACTCAGTGGGAAATTTCTGAACATGGGACCATCCCTGGGAGTGGGCCTGGGTCTCATCCTTATACCCTCACTAGGATCT
ATGTTTCTTCCACCTACCACCCACTGTGGC

Alignment

ORF - retro_amel_336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.57 %
• Parental protein coverage: 65.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TKTRVGIRRGKIGQELKEAAMEPSVEKIFKIDQMGRWVIAGGAAVGLGALCYYGLGMSNEIGAIEKAVIW
          T..R.GI..GK.GQE.KEA..EPS.EK..............G...GLGAL.YYGLG..NEI..IEKAVIW
Retrocopy THQRTGIWCGKAGQEPKEAVLEPSIEKYLNLIR*EDGLLLDGL-LGLGALFYYGLGIYNEIVTIEKAVIW

Parental  PQYVKDRIHSTYMYLAGSIGLTALSALAVSRTPILMNFMMRGSWVTIGATFAAM-IGAGMMVQSIPYDQS
          P.YVK.R.HS...YLAGSIG.TALS.L.V.RT..LMN.M.RGSWV..GATF.A..IG.GM.VQSI.YDQS
Retrocopy PRYVKNRNHSMHIYLAGSIGFTALSTLEVNRT-LLMN-MIRGSWVRTGATFEAI<IGGGMLVQSILYDQS

Parental  P-GPKHLAWLLHSGVMGAVVAPLT-ILGGPLLIRAAWYTAGIVGGLSTVAMCAPSEKFLNMGAPLGVGLG
          P..PK.LA.L..S.V.G...APLT.....PLLIRAA.YT.G...G.ST.A.CA.S.KFLNMG..LGVGLG
Retrocopy P>DPKELA*LFYSSVKGPIMAPLT>XXXXPLLIRAA*YTVGLGRGPSTLATCALSGKFLNMGPSLGVGLG

Parental  LVFVSSLGSMFLPPTTVAG
          L....SLGSMFLPPTT..G
Retrocopy LILIPSLGSMFLPPTTHCG

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_336 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_336 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 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009753	1 retrocopy	retro_amel_336 ,
Bos taurus	ENSBTAG00000032829	2 retrocopies	retro_btau_1689, retro_btau_779,
Choloepus hoffmanni	ENSCHOG00000001576	1 retrocopy	retro_chof_5,
Cavia porcellus	ENSCPOG00000006432	1 retrocopy	retro_cpor_1436,
Dasypus novemcinctus	ENSDNOG00000018880	5 retrocopies	retro_dnov_2426, retro_dnov_2514, retro_dnov_2524, retro_dnov_708, retro_dnov_812,
Dipodomys ordii	ENSDORG00000001109	1 retrocopy	retro_dord_184,
Echinops telfairi	ENSETEG00000001796	1 retrocopy	retro_etel_68,
Loxodonta africana	ENSLAFG00000009646	1 retrocopy	retro_lafr_388,
Macropus eugenii	ENSMEUG00000009861	3 retrocopies	retro_meug_1431, retro_meug_1806, retro_meug_798,
Microcebus murinus	ENSMICG00000011621	1 retrocopy	retro_mmur_692,
Monodelphis domestica	ENSMODG00000001693	3 retrocopies	retro_mdom_1008, retro_mdom_407, retro_mdom_886,
Oryctolagus cuniculus	ENSOCUG00000006093	1 retrocopy	retro_ocun_260,
Otolemur garnettii	ENSOGAG00000012120	1 retrocopy	retro_ogar_1287,
Rattus norvegicus	ENSRNOG00000013961	1 retrocopy	retro_rnor_2461,
Sus scrofa	ENSSSCG00000010345	1 retrocopy	retro_sscr_1102,
Tupaia belangeri	ENSTBEG00000016365	2 retrocopies	retro_tbel_1601, retro_tbel_2819,
Tarsius syrichta	ENSTSYG00000006367	1 retrocopy	retro_tsyr_4,
Drosophila melanogaster	FBgn0030263	1 retrocopy	retro_dmel_61,