RetrogeneDB ID: retro_etel_1992

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_322359:550..973(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RWDD1
• Ensembl ID: ENSETEG00000019085
• Aliases: None
• Description: RWD domain containing 1 [Source:HGNC Symbol;Acc:20993]

Sequence

>retro_etel_1992
TATATAGTATTCACAGAAAATCCACCCACTTTCACCATCACTGTGACATCTGAGGCTGGGAAAACAACTCCCTGGTGCAG
ACTGCACTCAAGTTTACAGACAGCAAAATTATCCAGATGATGCGCCCCTTTATGAAATAGCCCCCCAGGAAAGTCCAGCA
GATAATGATGTTTCAGACATTTAAAAATTATCACAATTACACGCAGAAGAAAAGCTTAGCCTGGGAATGAACTCTACTTT
TGTATCGACTGTGCAAGGAAAATGAAATGAAATAGTGGATCAAATAAGAGCCAGAAGAGAGGAAGACGAGAAAAGGAAGC
AGAGGAAGCTGAGCAGCAGCTTTTTCATGACACTCCTGTTACAAGGGAGACGCCCAGACTTTGGGAGACCAAATCTGGTG
AGGAACTCTTGGACATGAAAAAG

Alignment

ORF - retro_etel_1992 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.11 %
• Parental protein coverage: 60.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FTVLSERPSSFTITVTSEAG-ENNKTVQTTLKFTYS-EKYPDDAPLYEIFSQENLAENDVADILKLLALQ
          ..V..E.P..FTITVTSEAG.ENN..VQT.LKFT.S...YPDDAPLYEI..QE..A.NDV.DI.KL..L.
Retrocopy YIVFTENPPTFTITVTSEAG<ENNSLVQTALKFTDS<QNYPDDAPLYEIAPQESPADNDVSDI*KLSQLH

Parental  AEENLGMVMIFTLVSAVQEKLNEIVDQIKSRREEEKKQKEK-EAEEAEKQLFHGTPVTIENFLSWKAKFD
          AEE.L...M..T.VS.VQ.K.NEIVDQI..RREE..K.K...EAE....QLFH.TPVT.E....W..K..
Retrocopy AEEKLSLGMNSTFVSTVQGK*NEIVDQIRARREEDEKRKQR<EAEQ---QLFHDTPVTRETPRLWETKSG

Parental  AELSEKKR
          .EL...K.
Retrocopy EELLDMKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_1992 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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,