RetrogeneDB ID: retro_amel_991

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192802.1:823054..823606(-)
• Located in intron of: ENSAMEG00000004206

Retrocopy information

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

Parental gene information

• Parental gene symbol: RWDD1
• Ensembl ID: ENSAMEG00000005692
• Aliases: None
• Description: RWD domain containing 1 [Source:HGNC Symbol;Acc:20993]

Sequence

>retro_amel_991
TATCTGTACAGTGACAAATACCCAGATGAAGCCCCTCTTTATGAAATATCCTCCCAGGAAAATCTACAAGATAATGATGT
CTCAGACATCTTGAAATGATTAACATTATAGGCAGAAGAAAATCTTGGTATGGTGATGATCTTTACTTTAGTGACAGTTC
GTGCAAGAAAAATTAAATGAAATAGATCAAATAAAAACTGGAAGAGAAGAAAAGAAAAAGAGCAAGCAGCAGAAGAATCT
GAAGAGCAATTATTTCACAGCACTCCTGGTACAAATGAGAATTGCTTAAGTTGAAAGGCCAAGTTCGTTGCAGAACTCTT
GGAAATGAAAAAGAAATGAACGAAAGAAGAATGAACAGGAAAAAATGAATTAAGTGGGAAAGAGCTATTTGAAACAGATC
ATAATCTTGACACAATGGATATCCAGTTTTTGGAGGATGCTGGAAACAATGCAGAGGTAGATGACTCTCTGTTCCAGGAA
ATGGAGGACTTCGAGCTAGAGGACAAGAAGGATGATGTGAACTACAATCCTGCCGACCCAGAGAGTGATCTA

Alignment

ORF - retro_amel_991 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.62 %
• Parental protein coverage: 77.37 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FTYSEKYPDEAPLYEIFSQENLEDNDVSDILKLLALQAEENLGMVMIFTLVTAVQEKLNEIVDQIKSRRE
          ..YS.KYPDEAPLYEI.SQENL.DNDVSDILK.L.L.AEENLGMVMIFTLVT........I.........
Retrocopy YLYSDKYPDEAPLYEISSQENLQDNDVSDILK*LTL*AEENLGMVMIFTLVTV---RARKIK*NRSNKNW

Parental  EEKKQKEKEAEEAEKQLFHGTPVTIENFLSWKAKFDAELLEIKKKRMKEEEQAGKNKLSGKQLFETDHNL
          ...K.KE..AEE.E.QLFH.TP.T.EN.LS.KAKF.AELLE.KKK..KEE...GKN.LSGK.LFETDHNL
Retrocopy KRRKEKEQAAEESEEQLFHSTPGTNENCLS*KAKFVAELLEMKKK*TKEE*-TGKNELSGKELFETDHNL

Parental  DTSDIQFLEDAGNNVEVDESLFQEMDDLDLEDDGDGPDYTPADPESDL
          DT.DIQFLEDAGNN.EVD.SLFQEM.D..LED..D...Y.PADPESDL
Retrocopy DTMDIQFLEDAGNNAEVDDSLFQEMEDFELEDKKDDVNYNPADPESDL

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_991 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_991 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005692	1 retrocopy	retro_amel_991 ,
Bos taurus	ENSBTAG00000009689	1 retrocopy	retro_btau_1004,
Callithrix jacchus	ENSCJAG00000004474	1 retrocopy	retro_cjac_1622,
Equus caballus	ENSECAG00000006587	2 retrocopies	retro_ecab_216, retro_ecab_277,
Echinops telfairi	ENSETEG00000019085	3 retrocopies	retro_etel_140, retro_etel_1992, retro_etel_423,
Loxodonta africana	ENSLAFG00000008170	1 retrocopy	retro_lafr_813,
Monodelphis domestica	ENSMODG00000017837	1 retrocopy	retro_mdom_1686,
Oryctolagus cuniculus	ENSOCUG00000013592	1 retrocopy	retro_ocun_691,
Procavia capensis	ENSPCAG00000005016	1 retrocopy	retro_pcap_114,
Ictidomys tridecemlineatus	ENSSTOG00000020231	2 retrocopies	retro_itri_121, retro_itri_365,
Ictidomys tridecemlineatus	ENSSTOG00000022124	1 retrocopy	retro_itri_596,
Tupaia belangeri	ENSTBEG00000002543	2 retrocopies	retro_tbel_2986, retro_tbel_4366,