RetrogeneDB ID: retro_etel_2089

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_53146:1434..2266(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000013512
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000017395
• Aliases: None
• Description: None

Sequence

>retro_etel_2089
AACTGCCTACAGAGGATAAAGGTGGAGAACGCTGAGGAAAACCACTGGCAGTTCTGGGAAATCCTCTTCACCATAGACAA
TTCCATCAGGTGGAGCATCAGGGACGTGCTCCATTTCCATGAGACCCTCTACCAGAAGGACACCCAGGGAAAGCTGCTCA
CAACTATCCTCAAGGAAAATGGGGTTGTCATGGGTATCAAGTTGGAACAAGGAGCAGCTCCTCTTGAAAGAACAAACAAA
CAAGCCACCATTCAAGGGCTTGACGGCCTCTCTGAGTGCTGCTCAGTACAAAAAGGATGGGGCTGACTTTGGGAAGTGGC
GGGCTGTGCTGAGGATCACTGACCAGTGTCCATCCAGCCTTGCTATCCAGGAGAATGCCAACGTGATGGCTCACTATACT
AGCGTCTGTCAACAAAATGGGTTGGTGCCCATTGTGAAACCAGACGTCATTCTTAATGGAGACCATAACCTGGAACACAG
CCAGTAGGTTAGTGAGAAGGTCCTGGCAGTTGTTTACAAGGCCTTCAGTGACCATCATGTTTACGTGGAGGGCACGCTTT
TAAAACCAAACATGGTAACTGATGGACATGCCCACACCAAATAATATACTCCAGAGCAAGTGGCTTTGGCCACTGTCACA
GCTCTCCATTGTACTGCTCCTGCAACTGTTCCAGGAATTTGCTTCTTGTCTGGTGGCATGGTGAACAGAATGCCACTCTC
AACCACACTGTTATCAATCTTTGCCCTCTACCAGAGCACTGGAAACTAAGTTTCTCTTATGGGTGGGCCCTGTGGGTCAG
TGCGCGTTGCTGCTTGGAATGACAATGCTGCA

Alignment

ORF - retro_etel_2089 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.02 %
• Parental protein coverage: 80.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NRLQRIQVENTEENRRQFREMLFSVDNSVNQSIGGVILFHETLYQKDSQGKLFKTILKEKGIVVGIKLDQ
          N.LQRI.VEN.EEN..QF.E.LF..DNS...SI..V..FHETLYQKD.QGKL..TILKE.G.V.GIKL.Q
Retrocopy NCLQRIKVENAEENHWQFWEILFTIDNSIRWSIRDVLHFHETLYQKDTQGKLLTTILKENGVVMGIKLEQ

Parental  GAAPLAGTNKESTIQGLDGLSARC-AQYKKDGADFGKWRAVLRIADQCPSNLAIQENANALARYASICQQ
          GAAPL..TNK..TIQGLDGLS..C.AQYKKDGADFGKWRAVLRI.DQCPS.LAIQENAN..A.Y.S.CQQ
Retrocopy GAAPLERTNKQATIQGLDGLS-EC>AQYKKDGADFGKWRAVLRITDQCPSSLAIQENANVMAHYTSVCQQ

Parental  NGLVPIVEPEVIPDGDHDMEHCQYVSEKVLAAVYKALNDHHVYLEGTLLKPNMVTAGHACTKKYTPEQVA
          NGLVPIV.P.VI..GDH..EH.Q.VSEKVLA.VYKA..DHHVY.EGTLLKPNMVT.GHA.TK.YTPEQVA
Retrocopy NGLVPIVKPDVILNGDHNLEHSQ*VSEKVLAVVYKAFSDHHVYVEGTLLKPNMVTDGHAHTK*YTPEQVA

Parental  MATVTALHRTVPAAVPGICFLSGGM-SEEDATLNLNAINLCPLPKPWKLSFSYGRALQASA-LSAWNGKA
          .ATVTALH.T.PA.VPGICFLSGGM..E..ATLN...INLCPLP..WKLSFSYG.AL..SA...AWN..A
Retrocopy LATVTALHCTAPATVPGICFLSGGM<GEQNATLNHTVINLCPLPEHWKLSFSYGWALWVSA>VAAWNDNA

Parental  A
          A
Retrocopy A

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_2089 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 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014816	5 retrocopies	retro_dnov_1625, retro_dnov_1631, retro_dnov_2028, retro_dnov_2152, retro_dnov_547,
Echinops telfairi	ENSETEG00000017395	2 retrocopies	retro_etel_2089 , retro_etel_945,
Echinops telfairi	ENSETEG00000019230	1 retrocopy	retro_etel_20,
Monodelphis domestica	ENSMODG00000014418	2 retrocopies	retro_mdom_1752, retro_mdom_393,
Tupaia belangeri	ENSTBEG00000009298	1 retrocopy	retro_tbel_3244,