RetrogeneDB ID: retro_amel_460

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192452.1:2393075..2393490(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HINT1
• Ensembl ID: ENSAMEG00000017774
• Aliases: None
• Description: histidine triad nucleotide binding protein 1 [Source:HGNC Symbol;Acc:4912]

Sequence

>retro_amel_460
TTCTCCCCAAGCCATCACAGAGGTGGGTAGCTGTAACAGCAGATGAGGTTGTGAGGCTCAGGTTGTCTAGCCTGAGAACA
ATGTGACCGTTGGGAAGATTATCTGCAAGGCAATCCCAGCCTAACTCATTTTTATGGGTGACTAGACTCTTGCTTTCCAT
GATATTTCCCTTTGCACACATACACATTTTCTGGTGATACTTCAGAAAAATATTTCTCAGATTTCTGTAGCAGAAAGTGA
TGATGATAAAAGGTTTTTCTTGGGACATTTTATGATTGTTGGCAAGAAATGTGCTGTTGATCTGGGCTTGAAGAACTTAT
TGAATGGCGGTGAGGGAGAGTTTTATGGGGGATAGTCTGTCTACCATTTTCATCTCCATGTTCCTGGAAGTTAGCAGATG
AATTGGCCTCTCGGC

Alignment

ORF - retro_amel_460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.86 %
• Parental protein coverage: 99.28 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FSPGRSRGR-VAEMADEIAK-AQAARPGGDTIFGKIIRKEIPAKIIFEDDQCLAFHDISPQAPTHFLVIP
          FSP...RG..VA..ADE....AQ...P......GKII.K.IPA..IF..D..LAFHDIS....THFLVI.
Retrocopy FSPSHHRGG<VAVTADEVVR<AQVV*PENNVTVGKIICKAIPA*LIFMGD*TLAFHDISLCTHTHFLVIL

Parental  KKHISQISVAEDDDES--LLGHLMIVGKKCAADLGLKKGYRMVVNEGSD---GGQSVYHVHLHVLGGRQM
          .K.ISQISVAE.DD.....LGH.MIVGKKCA.DL....G.....N.G.....GG.SVYH.HLHV.G..QM
Retrocopy QKNISQISVAESDDDKRFFLGHFMIVGKKCAVDL----GLKNLLNGGEGEFYGG*SVYHFHLHVPGS*QM

Parental  NWPPG
          NWP.G
Retrocopy NWPLG

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_460 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_460 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 16 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017774	4 retrocopies	retro_amel_1426, retro_amel_1657, retro_amel_460 , retro_amel_511,
Bos taurus	ENSBTAG00000010959	5 retrocopies	retro_btau_1036, retro_btau_1149, retro_btau_1782, retro_btau_926, retro_btau_978,
Canis familiaris	ENSCAFG00000032152	1 retrocopy	retro_cfam_473,
Callithrix jacchus	ENSCJAG00000014398	3 retrocopies	retro_cjac_134, retro_cjac_142, retro_cjac_87,
Echinops telfairi	ENSETEG00000010127	1 retrocopy	retro_etel_1,
Gorilla gorilla	ENSGGOG00000011967	1 retrocopy	retro_ggor_89,
Macropus eugenii	ENSMEUG00000005368	2 retrocopies	retro_meug_1001, retro_meug_848,
Myotis lucifugus	ENSMLUG00000001091	2 retrocopies	retro_mluc_1388, retro_mluc_2100,
Monodelphis domestica	ENSMODG00000028727	3 retrocopies	retro_mdom_102, retro_mdom_1741, retro_mdom_286,
Mustela putorius furo	ENSMPUG00000011639	4 retrocopies	retro_mputfur_1337, retro_mputfur_1376, retro_mputfur_45, retro_mputfur_93,
Oryctolagus cuniculus	ENSOCUG00000006607	5 retrocopies	retro_ocun_1374, retro_ocun_214, retro_ocun_643, retro_ocun_821, retro_ocun_968,
Rattus norvegicus	ENSRNOG00000000622	1 retrocopy	retro_rnor_98,
Sarcophilus harrisii	ENSSHAG00000005834	2 retrocopies	retro_shar_113, retro_shar_301,
Sus scrofa	ENSSSCG00000014264	2 retrocopies	retro_sscr_371, retro_sscr_894,
Ictidomys tridecemlineatus	ENSSTOG00000027920	4 retrocopies	retro_itri_1129, retro_itri_114, retro_itri_177, retro_itri_260,
Tursiops truncatus	ENSTTRG00000008653	4 retrocopies	retro_ttru_1364, retro_ttru_1660, retro_ttru_217, retro_ttru_349,