RetrogeneDB ID: retro_gacu_21

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: groupXIV:8209776..8210713(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGACG00000017585
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSGACG00000017629
• Aliases: None
• Description: None

Sequence

>retro_gacu_21
GATGAAATAACTTTTCGAGACCGCTTTCGTATGCACAAGGAAAATGCATTGGAGATAATTACTTTGCTTGAGCCTAGACT
TTCCTCTCTGTCTCAAAGAGGAAGGCCTGTGTCCAATCAACTGCAAGTTCTGATCACTTTGAGGTTCTTGGCATGTGGAA
TCTTTCATCGTGAAACTGGTGATTTGTGTGGTGTCAGTGAACCAACTGTATGTAGAATAGTTCACAAAGTCTGCAGTGCC
ATTTGTGAACTGAGGAGTCTTTACATCAAGTTCCCTGATGCTGCTGGGCAAGCCAACTATAAAGTGCAATTCTATGAATA
TGGGCACTTTCCAGGAGTGATTGGCTGTATAGACGGATGTCATGTTCCCATCAAGTGTCCATCAACTCCTGATGCAGAGG
AATACAGGAATCGTAAGAACTGTTTTTCAATCAATGTTCAGGGTGTATGCACTCCTAATTTGGAGTTTTCAAACATTGTT
GCCCGTTGGAAAAGGTGCAACCCATGATTCAAGGATTTTTCTCAACTCTTCATTGTGTGCACAATTTGAGAGTGGACAAC
ATAGTGGACTACTACTTGGTGATAGTGGATATGGTCAGAGTAACTATTTATTCACACCACATCTAAATCCCACAACAGCT
GAGCAGCAAAGGTACAACAGAGCTCATATCCGTACTAGAGGGATGATCGAGCGTATGTTTGGAGTATGGAAAACTCGATT
CCAGTGCTTACGAAATACGATTCGTTTCAAGCCAAGAAGATGCTGCAAAGTGATCATTGCTACAGCTGTGCTGCACAACT
ACCTGAAGCAGCATGGCTGTCCTGACCTGCCAATGGAAGATCAGGATGATGCAGATGTGCCCATGGTGGCAGAGGCAGCC
AATGACCAGCGAGGACTTGCACACAGAGCTGCTTTCACAGTGCAGCACTTCAGCATT

Alignment

ORF - retro_gacu_21 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.93 %
• Parental protein coverage: 98.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NEEVVEGRFKTCTENMFGLFFPLKPRLSSLSQRGRPVSNQLQVLITLRFLACGIFHRETGDLCGVSEPTV
          .E.....RF....EN.......L.PRLSSLSQRGRPVSNQLQVLITLRFLACGIFHRETGDLCGVSEPTV
Retrocopy DEITFRDRFRMHKENALEIITLLEPRLSSLSQRGRPVSNQLQVLITLRFLACGIFHRETGDLCGVSEPTV

Parental  CRIVHKVCSAICELRSLYIKFPDAAGQANYKVQFYEYGHFPGVIGCIDGCHVPIKCPSTPDAEEYRNRKN
          CRIVHKVCSAICELRSLYIKFPDAAGQANYKVQFYEYGHFPGVIGCIDGCHVPIKCPSTPDAEEYRNRKN
Retrocopy CRIVHKVCSAICELRSLYIKFPDAAGQANYKVQFYEYGHFPGVIGCIDGCHVPIKCPSTPDAEEYRNRKN

Parental  CFSINVQGVCTPNLEFSNIVARW-KGATHDSRIFLNSSLCAQFESGQHSGLLLGDSGYGQSNYLFTPHLN
          CFSINVQGVCTPNLEFSNIVARW.KGATHDSRIFLNSSLCAQFESGQHSGLLLGDSGYGQSNYLFTPHLN
Retrocopy CFSINVQGVCTPNLEFSNIVARW>KGATHDSRIFLNSSLCAQFESGQHSGLLLGDSGYGQSNYLFTPHLN

Parental  PTTAEQQRYNRAHIRTRGMIERMFGVWKTRFQCLRNTIRFKPRRCCKVIIATAVLHNYLKQHGCPDLPME
          PTTAEQQRYNRAHIRTRGMIERMFGVWKTRFQCLRNTIRFKPRRCCKVIIATAVLHNYLKQHGCPDLPME
Retrocopy PTTAEQQRYNRAHIRTRGMIERMFGVWKTRFQCLRNTIRFKPRRCCKVIIATAVLHNYLKQHGCPDLPME

Parental  DQDDADVPMVAEAANDQRGLAHRAAFTVQHFSI
          DQDDADVPMVAEAANDQRGLAHRAAFTVQHFSI
Retrocopy DQDDADVPMVAEAANDQRGLAHRAAFTVQHFSI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Gasterosteus aculeatus was not studied using RNA-Seq expression data.

ChIP-Seq

Gasterosteus aculeatus was not studied using ChIP-Seq data.

EST

Gasterosteus aculeatus was not studied using EST data.

TSS

Gasterosteus aculeatus was not studied using FANTOM5 data.

Lab

retro_gacu_21 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_21 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000017629	1 retrocopy	retro_gacu_21 ,
Gadus morhua	ENSGMOG00000009026	1 retrocopy	retro_gmor_19,
Gadus morhua	ENSGMOG00000012106	1 retrocopy	retro_gmor_30,