RetrogeneDB ID: retro_etel_203

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_353:358932..359572(-)
• Located in intron of: ENSETEG00000013613

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB2A
• Ensembl ID: ENSETEG00000010340
• Aliases: None
• Description: RAB2A, member RAS oncogene family [Source:HGNC Symbol;Acc:9763]

Sequence

>retro_etel_203
ATGGCGTACGCCTATCTCTTCTAGTACATCATCATTGGTGACACAGGTGTTGGCAAATCGTGCTTATTGCTACAGTTTAC
AGACAAGAGGTTTCAGCCTGTGCATGACCTTTACTATTGGTGTAGAGTTTGGTGCTCGAATGATAAACGATCGATAGAAA
ACAGATAAAAACTTCAGATATGGGATATGGGCAGGACAAGAGTCCTATTCGCTTCATCACAAAGGTCATATTACAGAGAA
GCAGCAGGTGCTTTACAAGTATATGATATTACAAGGAGAGATACATTCAACCATTTGACCACCTGGTTAGAAGATGCCTG
CCAGCATTCTAATTCCAACATGGTCATTATGCTTATTGGAAATAAAAGTGATTTAGAATCTAGAAGAGAAGTTAAAAAAG
AAGAAGGTGAAGCTTTTGCAAGAGGACATGGACTTATCTTCATGGAAACTTCTGCTAAGACTGCTTCCAATGTGGAAGAG
GCATTTATTAATACAGCAAAATAAAATTATGAAAAAATTCAAGGAGTATTTGACATTAATAATGAGGCAAATGGCATTAA
GATTGGCCCTCAGCATGCTGCTACTAATGCAACACATGCAGGCAGTCAGGGAGGACTAGCAGGCAGAAGGAGGCTGCTGC

Alignment

ORF - retro_etel_203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAYAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDL-TIGVEFGARMI-TIDGKQIK-LQIWDTAGQES
          MAYAYLF.YIIIGDTGVGKSCLLLQFTDKRFQPVHDL.TIGVEFGARMI.TID.KQIK.LQIWD......
Retrocopy MAYAYLF*YIIIGDTGVGKSCLLLQFTDKRFQPVHDL>TIGVEFGARMI>TIDRKQIK>LQIWDMGRTRV

Parental  -FRSITRSYYRGAAGALLVYDITRRDTFNHLTTWLEDARQHSNSNMVIMLIGNKSDLESRREVKKEEGEA
          .F.S..RSYYR.AAGAL.VYDITRRDTFNHLTTWLEDA.QHSNSNMVIMLIGNKSDLESRREVKKEEGEA
Retrocopy LFASSQRSYYREAAGALQVYDITRRDTFNHLTTWLEDACQHSNSNMVIMLIGNKSDLESRREVKKEEGEA

Parental  FAREHGLIFMETSAKTASNVEEAFINTAKEIYEKIQEGVFDINNEANGIKIGPQHAATNATHAGSQGGQ-
          FAR.HGLIFMETSAKTASNVEEAFINTAK..YEKIQ.GVFDINNEANGIKIGPQHAATNATHAGSQGG..
Retrocopy FARGHGLIFMETSAKTASNVEEAFINTAK*NYEKIQ-GVFDINNEANGIKIGPQHAATNATHAGSQGGL>

Parental  QAGDGCC
          QA..GCC
Retrocopy QAEGGCC

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_203 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 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007700	1 retrocopy	retro_eeur_496,
Echinops telfairi	ENSETEG00000004920	5 retrocopies	retro_etel_1150, retro_etel_2132, retro_etel_2214, retro_etel_694, retro_etel_837,
Echinops telfairi	ENSETEG00000010340	2 retrocopies	retro_etel_203 , retro_etel_32,
Echinops telfairi	ENSETEG00000018042	3 retrocopies	retro_etel_1163, retro_etel_122, retro_etel_681,
Monodelphis domestica	ENSMODG00000008556	2 retrocopies	retro_mdom_1999, retro_mdom_989,
Mus musculus	ENSMUSG00000047187	1 retrocopy	retro_mmus_2650,