RetrogeneDB ID: retro_etel_1488

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_273572:2421..3218(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: G3BP1
• Ensembl ID: ENSETEG00000017447
• Aliases: None
• Description: GTPase activating protein (SH3 domain) binding protein 1 [Source:HGNC Symbol;Acc:30292]

Sequence

>retro_etel_1488
TATGGAAAGAACTCTTCTTATGTCCATGGTGGCTTGGATTCAAATGGAAAACCAGCAGATGCTGTCTATGGACAAAAGGA
AATCCATAGGAAAGTTATGTCTCAAAACTTTACTAACTGCCACACTAAGATTCGCCATGTTGATGCTCATGCTACTCTCA
ATGATGGTGTGGTGTCCAGGTGATGGGACTGCTGTCTAATAACAACCAGGCTCGGAGGAGATTCATGCAGACATTTGTCC
TTGCTCCTGAGGGCTCTGTTGCAAATACATTCTATGTTCACAATGATATCTTCAGATATCAAGATGAAGTTTTTGGTGGC
TTTGTCACCGAGCCTCAAGCGGAATCTGAAGAAGAAGTAGAGGAGCCTGAACAAAGACAGCAGACACCAGAGGTGGTACC
TGATGATGCTGGAGCATTTTATGAGCAGACTGTCAGCAATGACTTAGAGGAACATTTAGAGGAACCAGTTGCTGAACCAG
AGCCTGATCCTGAACCAGAACCAGAGCAAGAGCCCGTACCTGAAATCCAGGAGGAAAAATCTGAGCTTGCCTTAGAAGAA
ACTGCTCCTGAGGATGCTCAGAAGAGTCGTGTCGCGCCCCCCACCCCCCGCCCCTGCAGATGGGGCGCAGATGGGGCTCA
GACGGTGCAGGAAGACTTGAGGACATTTTCTTGGGCATCTGTGACCAGTAAGAACCTTCCACCCAGTGGAGCTGTTCCAG
TTACTGGGATTCCACCTCATGTTGTCAAAGTCCCAGCTTCACAGCCCCGACCTGAGTCTAAGCCTGAATCTCAGATA

Alignment

ORF - retro_etel_1488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.65 %
• Parental protein coverage: 59.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YGKNSSYVPGGLESNGKTADAVYGQKEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVV-VQVMGLLSNNN
          YGKNSSYV.GGL.SNGK.ADAVYGQKEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVV.VQVMGLLSNNN
Retrocopy YGKNSSYVHGGLDSNGKPADAVYGQKEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVV<VQVMGLLSNNN

Parental  QALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEVFGGFVTEPQEESEEEVDEPEERQQTPEVVPDDSGA
          QA.RRFMQTFVLAPEGSVAN.FYVHNDIFRYQDEVFGGFVTEPQ.ESEEEV.EPE.RQQTPEVVPDD.GA
Retrocopy QARRRFMQTFVLAPEGSVANTFYVHNDIFRYQDEVFGGFVTEPQAESEEEVEEPEQRQQTPEVVPDDAGA

Parental  FYDQTVSND----LEEHLEEPVAEPEPDPE----PEPEQEPVPEIQEEKSEPALEETAPEDAQKSSSPAP
          FY.QTVSND....LEE...EP...PEP.PE....PE...E......EE......................
Retrocopy FYEQTVSNDLEEHLEEPVAEPEPDPEPEPEQEPVPEIQEEKSELALEETAPEDAQKSRVAXXXXXXCRWG

Parental  ADGAQTVQEDLRTFSWASVTSKNLPPSGAVPVTGIPPHVVKVPASQPRPESKPESQI
          ADGAQTVQEDLRTFSWASVTSKNLPPSGAVPVTGIPPHVVKVPASQPRPESKPESQI
Retrocopy ADGAQTVQEDLRTFSWASVTSKNLPPSGAVPVTGIPPHVVKVPASQPRPESKPESQI

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_1488 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 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006626	2 retrocopies	retro_cpor_1119, retro_cpor_464,
Dasypus novemcinctus	ENSDNOG00000018758	3 retrocopies	retro_dnov_1492, retro_dnov_1632, retro_dnov_526,
Echinops telfairi	ENSETEG00000016219	1 retrocopy	retro_etel_86,
Echinops telfairi	ENSETEG00000017447	1 retrocopy	retro_etel_1488 ,
Oryctolagus cuniculus	ENSOCUG00000022143	1 retrocopy	retro_ocun_1352,
Rattus norvegicus	ENSRNOG00000013186	1 retrocopy	retro_rnor_1282,
Tupaia belangeri	ENSTBEG00000004386	12 retrocopies	retro_tbel_2177, retro_tbel_2295, retro_tbel_2296, retro_tbel_2327, retro_tbel_2352, retro_tbel_2460, retro_tbel_2461, retro_tbel_3889, retro_tbel_3928, retro_tbel_4180, retro_tbel_4190, retro_tbel_4246,
Tursiops truncatus	ENSTTRG00000009072	1 retrocopy	retro_ttru_70,