RetrogeneDB ID: retro_amel_600

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192519.1:957423..957973(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC2
• Ensembl ID: ENSAMEG00000012826
• Aliases: None
• Description: ER membrane protein complex subunit 2 [Source:HGNC Symbol;Acc:28963]

Sequence

>retro_amel_600
GTCAAGAGACTAACCGGCATGAGATTTGAAGCCACGGAAAGATATGATAATGCTATACAACTATATGATAGAATTTTACA
AGAAGATCCTACTAACAATGCTGCAAGAAAGCCTAAGCTTGCCGTTTGAAAGCCCAGGGGAAAAATGTGGAGGCCATTCT
GGAACTGAATGAGTACTGGAACAATTTGTTGGGGACCAACAAGCCTGACATTAACGTGCAGAACTTTGTATCAATGAACG
TGACTTTGCTAGAGCAGAGGAGCTAATGACGGCCAATCCACATGACCACTTACACTGTCAGCAGTATGCTGAAGTTAAAT
ATACCCAAGATGGACCTGGAAACCTCGAACTTTCAAGAAAGCATTTTGCACAGGCACTGAAACTCAACAACAGAAATATG
AGAGCTTTGTTTGGGCTTTACATGTTGGCAAGTCATATTGCTTCTAATCCAAAAGCAAGTGCAAAAACAAAAAAGGACAA
CATGAAATATGCTAGTTGGGCAGCTAGACAAATAAACAGAGCCTATCAATTTGCAGGTCGAAGAAGGAAA

Alignment

ORF - retro_amel_600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.11 %
• Parental protein coverage: 63.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VKRLTGMRFEAMERYDDAIQLYDRILQEDPTNTAARKRKIAI-RKAQGKNVEAIRELNEY-LEQFVGDQE
          VKRLTGMRFEA.ERYD.AIQLYDRILQEDPTN.AARK.K.A...KAQGKNVEAI.ELNEY.LEQFVGDQ.
Retrocopy VKRLTGMRFEATERYDNAIQLYDRILQEDPTNNAARKPKLAV<LKAQGKNVEAILELNEY<LEQFVGDQQ

Parental  AWHELAELYINEHDYAKAAFCLEELMMTNPHNHLYCQQYAEVKYTQGGLENLELSRKYFAQALKLNNRNM
          A.H..AEL.INE.D.A.A....EELM..NPH.HL.CQQYAEVKYTQ.G..NLELSRK.FAQALKLNNRNM
Retrocopy A*H*RAELCINERDFARA----EELMTANPHDHLHCQQYAEVKYTQDGPGNLELSRKHFAQALKLNNRNM

Parental  RALFGLYMSASHIASNPKASAKTKKDNMKYASWAASQINRAYQFAGRSKK
          RALFGLYM.ASHIASNPKASAKTKKDNMKYASWAA.QINRAYQFAGR..K
Retrocopy RALFGLYMLASHIASNPKASAKTKKDNMKYASWAARQINRAYQFAGRRRK

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_600 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_600 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012826	1 retrocopy	retro_amel_600 ,
Canis familiaris	ENSCAFG00000000713	1 retrocopy	retro_cfam_726,
Choloepus hoffmanni	ENSCHOG00000011271	3 retrocopies	retro_chof_1512, retro_chof_1990, retro_chof_851,
Callithrix jacchus	ENSCJAG00000006437	2 retrocopies	retro_cjac_3295, retro_cjac_3867,
Myotis lucifugus	ENSMLUG00000013258	2 retrocopies	retro_mluc_2369, retro_mluc_2452,
Mustela putorius furo	ENSMPUG00000005915	1 retrocopy	retro_mputfur_1647,
Mus musculus	ENSMUSG00000022337	1 retrocopy	retro_mmus_1262,
Oryctolagus cuniculus	ENSOCUG00000002461	1 retrocopy	retro_ocun_1251,
Pongo abelii	ENSPPYG00000018820	1 retrocopy	retro_pabe_1600,