RetrogeneDB ID: retro_etel_1843

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_306359:13699..14984(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000009816
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF5
• Ensembl ID: ENSETEG00000015220
• Aliases: None
• Description: eukaryotic translation initiation factor 5 [Source:HGNC Symbol;Acc:3299]

Sequence

>retro_etel_1843
ATGTCTGTTAACGTAAACCGCAGTGTGTCAGACCAGTTCTATCACTACAAGATGCCCCGTCTGATTGCCAAGGTTGAGGG
CAAAGGAAATGGAATCAAGACCGTTACAGTCAACATGGTTGACGTTGCAAAGGCGCTTAATGGGCCTCCAACATATCCCA
CCAAATATCTGGGTTGTGAGCTGGGAGCACAGACCCAGTTTGATGTTAAGAATGACCGTTACATTGTCAATGGATCGCAT
GAGGCGAATAAGCTGCAAGACATGTTGGACGGATTCATTAAAAAATTTGTTCTCTGTCCTGAGTGTGAAAATCCTGAAAC
AAATCTGCATGTCAATCCAAAGAAGCAAACAATAGGGAATTCTTGTAAAGCCTGTGGCTACCGAGGCATGCTTGACACAC
ATCATAAACTCTGCACATTCATTCTCAAAAACCCACCTGAGAATAGTGACAGCGGTACAGGAAAGAAGGAAAAGGAAAAG
AAGAACCGGAAGGGCAAAGACAAGGAGAGTGGCTCTGTGTCCAGCAGTGAAACACCACCGCCTCCACCTCCAAATGAAAT
CAGTCCTCCCCGTGCTGTGGAAGATGAGGGGGAGGATGCTTGGGGCGAGGACACAAGTGAGGAAGCACAGAGGCACAGAA
TGCATGAAATCAGTGACCAGGCCAAAGTCCCGGCCCTTAGTGACGATCTAGAGAGGACCATCGAGGAACGGGTTAACATC
CTGTTTGATTTTGTTAAGAAAAAGAAAGAAGAGGGTGTTATTGATTCTTCTGACAAAGAAATTGTTGCTGAAGCAGAAAG
ACTGGACGTAAAAGCCATGGGCCCCCTTGTTTTGACTGAAGTTCTTTTTAATGAGAAGATTAGGGAACACATCAAGAAGT
ACAGACGGCACGTCCTACGATTTTGACACAACAAAAAGGCCCAGCGGTACCTTCGGCATGGTTTGGAGTGTGTGGTGGCG
ATGCATCCAAGCTCAGCTCAGCTCCAAGGTCCCACACATCCTGAAGGAGATGGATGATGCAGACCTTTTGGAGGAAGAGG
TCATCATCAGCTGCTCCGAAAAGGCCTCAAAGAAATACGTCTCAAAAGAACTTGCCAAAGAGATTCGTGTCAAAGCTGAG
CCCTTCATAACATGGTTGAAGGAGGCAGAAGAGGAGTCTTCTGGTGGTGAAGAAGAAGATGAAGGAGAGAATATTGAGGT
GGTGTATTCGAAGACTGCCAGTGTACCCAAAGTTAAGACTGTGAAGTCTGACAACAAGGATGACGACATTGATATTGATG
CCATT

Alignment

ORF - retro_etel_1843 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVNVNRSVSDQFYRYKMPRLIAKVEGKGNGIKTVIVNMVDVAKALNRPPTYPTKYFGCELGAQTQFDVK
          MSVNVNRSVSDQFY.YKMPRLIAKVEGKGNGIKTV.VNMVDVAKALN.PPTYPTKY.GCELGAQTQFDVK
Retrocopy MSVNVNRSVSDQFYHYKMPRLIAKVEGKGNGIKTVTVNMVDVAKALNGPPTYPTKYLGCELGAQTQFDVK

Parental  NDRYIVNGSHEANKLQDMLDGFIKKFVLCPECENPETDLHVNPKKQTIGNSCKACGYRGMLDTHHKLCTF
          NDRYIVNGSHEANKLQDMLDGFIKKFVLCPECENPET.LHVNPKKQTIGNSCKACGYRGMLDTHHKLCTF
Retrocopy NDRYIVNGSHEANKLQDMLDGFIKKFVLCPECENPETNLHVNPKKQTIGNSCKACGYRGMLDTHHKLCTF

Parental  ILKNPPENSDSGTGKKEKEKKNRKGKDKENGSVSSSETPPPPPPNEISPPRAVEDEEDDDWGEDTTEEAQ
          ILKNPPENSDSGTG................GSVSSSETPPPPPPNEISPPRAVEDE..D.WGEDT.EEAQ
Retrocopy ILKNPPENSDSGTGXXXXXXXXXXXXXXXXGSVSSSETPPPPPPNEISPPRAVEDEGEDAWGEDTSEEAQ

Parental  RRRMDEISDHAKVLTLSDDLERTIEERVNILFDFVKKKKEEGVIDSSDKEIVAEAERLDVKAMGPLVLTE
          R.RM.EISD.AKV..LSDDLERTIEERVNILFDFVKKKKEEGVIDSSDKEIVAEAERLDVKAMGPLVLTE
Retrocopy RHRMHEISDQAKVPALSDDLERTIEERVNILFDFVKKKKEEGVIDSSDKEIVAEAERLDVKAMGPLVLTE

Parental  VLFNEKIREQIKKYRRHFLRFCHNNKKAQRYLLHGLECVVAMH-QAQLISKIPHILKEMYDADLLEEEVI
          VLFNEKIRE.IKKYRRH.LRF.H.NKKAQRYL.HGLECVVAMH.QAQL.SK.PHILKEM.DADLLEEEVI
Retrocopy VLFNEKIREHIKKYRRHVLRF*H-NKKAQRYLRHGLECVVAMH>QAQLSSKVPHILKEMDDADLLEEEVI

Parental  ISWSEKASKKYVSKELAKEIRVKAEPFIKWLKEAEEESSGGEEEDEDENIEVVYSKTASVPKVETVKSDN
          IS.SEKASKKYVSKELAKEIRVKAEPFI.WLKEAEEESSGGEEEDE.ENIEVVYSKTASVPKV.TVKSDN
Retrocopy ISCSEKASKKYVSKELAKEIRVKAEPFITWLKEAEEESSGGEEEDEGENIEVVYSKTASVPKVKTVKSDN

Parental  KDDDIDIDAI
          KDDDIDIDAI
Retrocopy KDDDIDIDAI

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_1843 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001236	1 retrocopy	retro_cpor_577,
Echinops telfairi	ENSETEG00000015220	2 retrocopies	retro_etel_1843 , retro_etel_991,
Monodelphis domestica	ENSMODG00000013424	1 retrocopy	retro_mdom_2000,
Rattus norvegicus	ENSRNOG00000010218	2 retrocopies	retro_rnor_1781, retro_rnor_2459,
Tursiops truncatus	ENSTTRG00000002384	1 retrocopy	retro_ttru_400,