RetrogeneDB ID: retro_etel_1275

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_239139:4453..5226(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000013168
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARPC1B
• Ensembl ID: ENSETEG00000009924
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 1B, 41kDa [Source:HGNC Symbol;Acc:704]

Sequence

>retro_etel_1275
GCTGTGTGCGTGCGCTGGGCGGCCCTGGAGAACAAGTTTGCTGTTGGCAGTGGCTCCCGCGTCATCGCCATCTGCTACTT
CGAGCAGGAGAATGACTGGTGGGTGTGCAAACACATCAAGAAGCCCATCCGCTCCACCGTCCTCAGCCTGGACCGGCACC
CCAGCAACGTGCTCCAGGCTGCCGGCTCCTGCGACTTTAAGTGCCGGATCTTCTCCGCCTACATCAGGGAGGTGGGGCAG
CGGCCGGCACCCACCCCATGGGGATCCCAGATGCCCCTTGGGGAGCTGATGTTTGGATCTAGCAGCAGCTGCGGCTGGGT
ACGCGGCGTCTGTTTCTCAGCAAGTGGGGGCCGAGTGGCCTGGGTCAGCCACGACAGCGCCGTGTGCCTGGCCAGTGCCG
ACAAGATGGCCGTCGCCACCCTGGCCTCTGGAACACTGCCCCTGCTGGCCGTCACCTTCATCCCAGAGAACAGTCTGGTG
GCAGCGGGTCACCACGGCTTCCCGGTGCTGTCCCCTACGACAGCGCGGTAGGGACGCGCGCGGAGCTTCGGGGGACGGCT
GGACGTGCCCAAGCAGAGCTCCCAGCGTGGCCTAACGGCCCGAGAGCGCTTCCAGAACGTGGACAAGGAGGCCAGCACAG
AGGGCGGTGCCGTCTCAGGGGCCGGGATCCACTCAGTGCACAAGCACAGTGCCAGCCAAAGCTCAGTACTCAGTGGGGGA
AGGCCCAGTGTGCACAATTCTGCACAACTGGCACGGACGGTGGCATGAGCCTG

Alignment

ORF - retro_etel_1275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.23 %
• Parental protein coverage: 69.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARCVRWAPLENKFAVGSGSRVISICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRI
          A.CVRWA.LENKFAVGSGSRVI.ICYFEQENDWWVCKHIKKPIRSTVLSLD.HP.NVL.AAGSCDFKCRI
Retrocopy AVCVRWAALENKFAVGSGSRVIAICYFEQENDWWVCKHIKKPIRSTVLSLDRHPSNVLQAAGSCDFKCRI

Parental  FSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHGVCFSASGSRVAWVSHDSTVCLANADKKMAVA
          FSAYI.EV..RPAPTPWGS.MP.GELMF.SSSSCGWV.GVCFSASG.RVAWVSHDS.VCLA.ADK.MAVA
Retrocopy FSAYIREVGQRPAPTPWGSQMPLGELMFGSSSSCGWVRGVCFSASGGRVAWVSHDSAVCLASADK-MAVA

Parental  TLASETLPLLAVTFITENSLVAAGHDCFPVLFTYDSTVGTL-SFGGRLDVPKQSSQRGLTARERFQNLDK
          TLAS.TLPLLAVTFI.ENSLVAAGH..FPVL.......G...SFGGRLDVPKQSSQRGLTARERFQN.DK
Retrocopy TLASGTLPLLAVTFIPENSLVAAGHHGFPVLSPTTAR*GRARSFGGRLDVPKQSSQRGLTARERFQNVDK

Parental  KASTEGGAVSGAGIDSVHKNSVSQISVLRG-GKAQCAQFCTTGMDGGMSI
          .ASTEGGAVSGAGI.SVHK.S.SQ.SVL.G.GKAQCAQFCTTG.DGGMS.
Retrocopy EASTEGGAVSGAGIHSVHKHSASQSSVLSG<GKAQCAQFCTTGTDGGMSL

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_1275 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046248	2 retrocopies	retro_btau_1547, retro_btau_473,
Canis familiaris	ENSCAFG00000015081	1 retrocopy	retro_cfam_1568,
Callithrix jacchus	ENSCJAG00000015849	1 retrocopy	retro_cjac_2365,
Echinops telfairi	ENSETEG00000009924	2 retrocopies	retro_etel_1076, retro_etel_1275 ,
Gorilla gorilla	ENSGGOG00000013186	2 retrocopies	retro_ggor_1337, retro_ggor_1455,
Microcebus murinus	ENSMICG00000017424	1 retrocopy	retro_mmur_602,
Myotis lucifugus	ENSMLUG00000010933	1 retrocopy	retro_mluc_974,
Mustela putorius furo	ENSMPUG00000016522	1 retrocopy	retro_mputfur_1578,
Mus musculus	ENSMUSG00000029622	2 retrocopies	retro_mmus_1340, retro_mmus_3623,
Otolemur garnettii	ENSOGAG00000010872	2 retrocopies	retro_ogar_2380, retro_ogar_3087,
Rattus norvegicus	ENSRNOG00000000991	2 retrocopies	retro_rnor_1105, retro_rnor_967,
Sus scrofa	ENSSSCG00000007625	1 retrocopy	retro_sscr_374,