RetrogeneDB ID: retro_etel_2178

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_89011:2..1294(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000017751
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CAPRIN1
• Ensembl ID: ENSETEG00000009308
• Aliases: None
• Description: cell cycle associated protein 1 [Source:HGNC Symbol;Acc:6743]

Sequence

>retro_etel_2178
ACTGACTTGAAGCAAGGCTTGAATGGCGTGCCGATATTCTCTGAAGAGGAATTGACCTTGTTGGATGATTTCTACAAACG
AGTGGACCCTGACCGAGACGTGAGCTTAAGATTGAATGAGCAGTGTGAGCATGTCTCCGTTCACCTGTGGGACCTGCTGG
AGGGGAAGGAAAATCTGTATGTGGAACAAGCTAGAAAGCACTAAAGGAAATTGTTGAGCGGGTTTTTCAGTCAAACTACT
TTGACAGTACCCACAACCACCAAAATGGGTTATGTGAGGAAGAGGAGGCTGCCTCAACACCCACATTGAAGACCAGGGAG
CTGAAGCTGAACCCGAGCCAGCAGAGGCATACACTGAACAGAATGAAGTTGAATCAACAGAGTAGTACGTAAATAGACAA
TGTATGGCAGAAACACCGTTCTGCAGTGGTGAAAAAGAGCAAGTAGATGAGTGGTCAGTTGAACCAGTTGAGGTAGTAAA
TTCACTCCAACAGCAACCACAGGCTGCATGTCCTTCAGTACCAGAGCCCCACACTTTGACTCCAGTGGCTCAGGCAGATC
CCCTCGTGAGAAGACAGCGAGTACAAGACCTTATGGCACAAATGCAGGGGCTGTATAATTTCATTCAGGAATCTATGTTG
GATTTTGAAATCCAGACACTGGATCCTGCCATTGTATCTGCACAGCCCATGAATCCTACACAAAACCTGGACGTGTCCCA
GCTTGTGTGTCCTCCAGTTCATTCTGAATCCAGACTTGCTCAAGCTAATCAAGTTCCCGTACAACCCGAAGCTACCCAGG
TTCCTTCGGTTTCATCCACAAGTGAAGGGTACACATCATCTCAGCCCTCGTATCAGCCTTCTCATGCTGCAGAGCTGCGA
CCACAAAAGGAACTGATTGACCAGTTTCAGGCAACGATCTCTTTAAATACAGACCAGACTACAGCATCATCATCCCTTCC
AGCTGCATCTCAGCTTCAGGTGTTCCAGGCTGGGACAAGCAAACCTTTGCACAGCAGTGGAATCAATGTGAATGCAGCTC
CATTCCAGACCATGCAGACGGTGTTTAATATGAATGCCCCAGTACCTCCTGTTAATGAACCAGAGACTTTGAAGCAGCAA
AGTCAGTACCAAGCCAGTTATAACCACCAGAGCTTTTCCAATCAACCTCACCAAGTAGAACAAACAGAGCTTCAGCAAGA
ACAGCTTCAAACAGTGGTCGGCACTTACCATGGTTCCCAGGACCAGCCCCATCAAGTGACTGGCAACCATCAGCGGCCTC
CCCCAGCAGAAT

Alignment

ORF - retro_etel_2178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.93 %
• Parental protein coverage: 67.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TDLKQGLNGVPILSEEELTLLDDFYKLVDPERDMSLRLNEQYEHASVHLWDLLEGKE-KSVCGTTYKALK
          TDLKQGLNGVPI.SEEELTLLDDFYK.VDP.RD.SLRLNEQ.EH.SVHLWDLLEGKE.KSVCGT..KALK
Retrocopy TDLKQGLNGVPIFSEEELTLLDDFYKRVDPDRDVSLRLNEQCEHVSVHLWDLLEGKE<KSVCGTS*KALK

Parental  EIVERVFQSNYFDSTHNHQNGLCEEEEAASAPA-IEEQGAEAEPEPAEEYTEQNEVESTE-YVNRQFMAE
          EIVERVFQSNYFDSTHNHQNGLCEEEEAAS.P..IE.QGAEAEPEPAE.YTEQNEVESTE.YVNRQ.MAE
Retrocopy EIVERVFQSNYFDSTHNHQNGLCEEEEAASTPT<IEDQGAEAEPEPAEAYTEQNEVESTE*YVNRQCMAE

Parental  TQFSSGEKEQVDEWTVETVEVVNSLQQQPQAASPSVPEPHTLTPVAQADPLVRRQRVQDLMAQMQGPYNF
          T.F.SGEKEQVDEW.VE.VEVVNSLQQQPQAA.PSVPEPHTLTPVAQADPLVRRQRVQDLMAQMQG.YNF
Retrocopy TPFCSGEKEQVDEWSVEPVEVVNSLQQQPQAACPSVPEPHTLTPVAQADPLVRRQRVQDLMAQMQGLYNF

Parental  IQDSMLDFENQTLDPAIVSAQPMNPTQNMDMPQLVCPPVHSESRLAQPNQVPVQPEATQVPLVSSTSEGY
          IQ.SMLDFE.QTLDPAIVSAQPMNPTQN.D..QLVCPPVHSESRLAQ.NQVPVQPEATQVP.VSSTSEGY
Retrocopy IQESMLDFEIQTLDPAIVSAQPMNPTQNLDVSQLVCPPVHSESRLAQANQVPVQPEATQVPSVSSTSEGY

Parental  TSSQPLYQSSHATEQRPQKEPIDQIQASSATISLNTDQTTTSSSLPAASQPQVFQAGTSKPLHSSGINVN
          TSSQP.YQ.SHA.E.RPQKE.IDQ.QA...TISLNTDQTT.SSSLPAASQ.QVFQAGTSKPLHSSGINVN
Retrocopy TSSQPSYQPSHAAELRPQKELIDQFQA---TISLNTDQTTASSSLPAASQLQVFQAGTSKPLHSSGINVN

Parental  AAPFQSMQTVFNMNAPVPPVNEPETLKQQSQYQASYN-QSFSNQPHQVEQTELQQEQLQTVVGTYHGSQD
          AAPFQ.MQTVFNMNAPVPPVNEPETLKQQSQYQASYN.QSFSNQPHQVEQTELQQEQLQTVVGTYHGSQD
Retrocopy AAPFQTMQTVFNMNAPVPPVNEPETLKQQSQYQASYNHQSFSNQPHQVEQTELQQEQLQTVVGTYHGSQD

Parental  QPHQVTGNHQQP-PQQN
          QPHQVTGNHQ.P.PQQN
Retrocopy QPHQVTGNHQRP>PQQN

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_2178 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000009308	1 retrocopy	retro_etel_2178 ,