RetrogeneDB ID: retro_gacu_22

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: groupXIX:20176432..20177311(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGACG00000014116
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: zgc:85777
• Ensembl ID: ENSGACG00000006126
• Aliases: None
• Description: zgc:85777 [Source:ZFIN;Acc:ZDB-GENE-040426-2210]

Sequence

>retro_gacu_22
ATGCAGACGGACATGGCCACCCCTGCACTGGCCAGGTTTGGTTCAGCCGAGCTAAAGGAAGAGTTCCTCCTTCCCTCCAT
CGCGGGGGACAAAGTGGCCTGCCTCGGGGTCAGTGAAGTCGGAGCCGGCTCTGATGTCTCAAGTATCCTGACAAAGGCAG
TGAAGAAAGGGGATGAATATGTGATCAACGGGGGGAAGATGTGGACCACCAACGGTACCCAGGCCTGGATATGGATACGT
CTCCTCGCCAACACAAGCGACGGGCCCCCACACAGGAACAAGTCCCTCATCTGTTTGCCCATGCACCTGCCAGGAGTCCA
CAAGATTGAGAAACTCGGCATGTGGTCGTCGGACACGGCCGAAGTGTTCTTCGATGACGTCCGTGTGCCCTGCAAGAGCA
TCGTTGGCCAGGAAGGCATGGGCTTCACCTATCAGATGCTTCAGTTCCAGGAGGAGCAGCTCTGGGCTGTGGGCAATATC
GTGACCATGATGGACAACATCATTCAGGAGACCATCCAGTACACCCGGCAGAGGAAGATCTTCAAGCTGCCCGTCCTCTA
CTACCAATCAGTTAACTTCAGGTTGGCCGAGCTGCAGACGGAGGTGGAGCTGCTCCGCTCCCTCCTCCACCGTGCCACAG
CATTGTACATTAAAGGCAACGATGTCACCAAACTGGCATCCATGGCCAAGTTAAAGACCGGCCGTCTGGCCAGGGAGGTG
GGCGACAGCTGCCTCCAGTATTGGGGAGGCATGGGCTTCACCAGCGACATGCTTGTCAGCAGATTCTACAGAGATTCTAG
GTTACTTTCAATTGGTGGAGGTACCGATGAGGTGATGCTGGTAATCATCTGCAAATACATGGACACACTAGCCAAGAAA

Alignment

ORF - retro_gacu_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.59 %
• Parental protein coverage: 75.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VQTDMATPALARFGSAELKEEFLLPSIAGDKVACLGVSEVGAGSDVSSILTKAVKKGDEYVINGGKMWTT
          .QTDMATPALARFGSAELKEEFLLPSIAGDKVACLGVSEVGAGSDVSSILTKAVKKGDEYVINGGKMWTT
Retrocopy MQTDMATPALARFGSAELKEEFLLPSIAGDKVACLGVSEVGAGSDVSSILTKAVKKGDEYVINGGKMWTT

Parental  NGTQA-DWICLLANTSDGPPHRNKSLICLPMNLPGVHIARKIEKLGMWSSDTAEVFFDDVRVPCKNIVGQ
          NGTQA..WI.LLANTSDGPPHRNKSLICLPM.LPGVH...KIEKLGMWSSDTAEVFFDDVRVPCK.IVGQ
Retrocopy NGTQAWIWIRLLANTSDGPPHRNKSLICLPMHLPGVH---KIEKLGMWSSDTAEVFFDDVRVPCKSIVGQ

Parental  EGMGFTYQMLQFQEERLWAVGNIVTMMDNIIQETIQYTRQRKIFKLPVLYHQSVNFRLAELQTEVELLRS
          EGMGFTYQMLQFQEE.LWAVGNIVTMMDNIIQETIQYTRQRKIFKLPVLY.QSVNFRLAELQTEVELLRS
Retrocopy EGMGFTYQMLQFQEEQLWAVGNIVTMMDNIIQETIQYTRQRKIFKLPVLYYQSVNFRLAELQTEVELLRS

Parental  LLHRATALYIKGNDVTKLASMAKLKAGRLAREVGDSCLQYWGGMGFTSDVLVSRFYRDSRLLSIGGGADE
          LLHRATALYIKGNDVTKLASMAKLK.GRLAREVGDSCLQYWGGMGFTSD.LVSRFYRDSRLLSIGGG.DE
Retrocopy LLHRATALYIKGNDVTKLASMAKLKTGRLAREVGDSCLQYWGGMGFTSDMLVSRFYRDSRLLSIGGGTDE

Parental  VMLAIICKYMDTLPKK
          VML.IICKYMDTL.KK
Retrocopy VMLVIICKYMDTLAKK

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_22 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_22 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000000487	1 retrocopy	retro_etel_761,
Gasterosteus aculeatus	ENSGACG00000006126	1 retrocopy	retro_gacu_22 ,