RetrogeneDB ID: retro_ggal_24

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: Z:7435362..7436300(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIAS2
• Ensembl ID: ENSGALG00000001843
• Aliases: None
• Description: E3 SUMO-protein ligase PIAS2 [Source:RefSeq peptide;Acc:NP_001025797]

Sequence

>retro_ggal_24
CTCTATAGGTGTAGGTACCCGTAGACAATCAAAGGACTTTTGGATTTATCAGCTATAAAACCTGCTGTTTTTCATCTGGA
CAGCAGTTCCTCTCCCACAGACCCTGTGTGGGATATTGCTGGGATTCACCCACTCCCTTCTGCTTTAGTCACACCTCAGT
TTCCTTCCTTGCCTGTCACCTTCATGCTCCTGCAAGACACTAAGGCTCACTTTGAGATGCAGCAGCCATCCCCTTCCATC
CCACCTGCCCATCCTGACATCCAGCTGAAAAGCCTGCCTTTTTACAATGTGCTTGATGTACTACTACTTAACAAGCCTAC
AAGTTTAGTACAGAGCAGTATTCAGAGGTTCCAAGAATAGTTTTTCCTCTTTGCTTTAACACCTCAGCAGGTCAGAGAAA
TTTGTATTTCCAGGGACTTCTTTCCAGGGGACAAAAGAGATTACCAAGTCCAAGTGCAGCTAAGATTATGGCAAGCAGAG
ACAAACTGCCCTCAAGAAGATAATTACCCTAACAGTTTGTGCATTAAAGTAAATTGGAAGCTGTTTCCATTGCTGGATAT
GCTCCACCAAATGGAATTAAACAGAAGGAATCTGGATGCCCCTTGAATATAACATCTCTAGATAGGCTGTTGTCAGCAGT
GCCAGAATAGATTTCTATTTCCTGGGCTTCTGAAATTGGAAAGAATTACTCAATGTCTCTGTATCTCATATGTCATCTCA
CTTCAGCTATGCTTTTGCAGAGGGTAAAAGTGAAAGGTATCCAAAACCCTGATTATTCTAGAGCTCTAATTAAAGAAGAA
CTAAGTACGGATCCTAACTGCAGACTGGCAAGTTCACTGTCATCTCTGATGTACTCTCTGTGAAAAATGAGACTGTCAAT
CCCTACTTGCACACACCTGCAATGTTTTGATGCTACTCTTCATCTTCAAATGAATGAT

Alignment

ORF - retro_ggal_24 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.47 %
• Parental protein coverage: 51.29 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LYRRRYPRTIEGLSDLSAIKPAVFSLDSSSSPVEPDLAVAGIHPLPSTSVTPQSPSSPVSSVLLQDTKAH
          LYR.RYP.TI.GL.DLSAIKPAVF.LDSSSSP..P....AGIHPLPS..VTPQ.PS.PV...LLQDTKAH
Retrocopy LYRCRYP*TIKGLLDLSAIKPAVFHLDSSSSPTDPVWDIAGIHPLPSALVTPQFPSLPVTFMLLQDTKAH

Parental  FEMQQPSPPIPPVHPDVQLKSLPFYDVLDVLI--KPTSLVQSSIQRFQEKFFIFALTPQQVREICISRDF
          FEMQQPSP.IPP.HPD.QLKSLPFY.VLDVL...KPTSLVQSSIQRFQE.FF.FALTPQQVREICISRDF
Retrocopy FEMQQPSPSIPPAHPDIQLKSLPFYNVLDVLLLNKPTSLVQSSIQRFQE*FFLFALTPQQVREICISRDF

Parental  LPGGRRDYTVQVQLRLCLAETSCPQEDNYPNSLCIKVNGKLFPL-PGYAPPPKNGIEQKRPGRPLNITSL
          .PG..RDY.VQVQLRL..AET.CPQEDNYPNSLCIKVN.KLFPL..GYAPP..NGI.QK..G.PLNITSL
Retrocopy FPGDKRDYQVQVQLRLWQAETNCPQEDNYPNSLCIKVNWKLFPL<AGYAPP--NGIKQKESGCPLNITSL

Parental  VRLSSAVPNQISISWASEIGKSYSMSVYLVRQLTSAMLLQRLKMKGIRNPDHSRALIKEKLTADPDSEIA
          .RL.SAVP..ISISWASEIGK.YSMS.YL...LTSAMLLQR.K.KGI.NPD.SRALIKE.L..DP....A
Retrocopy DRLLSAVPE*ISISWASEIGKNYSMSLYLICHLTSAMLLQRVKVKGIQNPDYSRALIKEELSTDPNCRLA

Parental  TTSLRVSLMCPLGKMRLTIPCRAVTCTHLQCFDAALYLQMNE
          ..S...SLM..L.KMRL.IP....TCTHLQCFDA.L.LQMN.
Retrocopy --SSLSSLMYSL*KMRLSIP----TCTHLQCFDATLHLQMND

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	6.83 RPM	20.43 RPM
SRP007412_cerebellum	8.37 RPM	37.94 RPM
SRP007412_heart	4.88 RPM	7.99 RPM
SRP007412_kidney	7.75 RPM	12.95 RPM
SRP007412_liver	4.57 RPM	6.57 RPM
SRP007412_testis	2.11 RPM	15.51 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ggal_24 retrocopy.

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_24 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_24 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005911	1 retrocopy	retro_chof_549,
Callithrix jacchus	ENSCJAG00000008117	1 retrocopy	retro_cjac_4167,
Gallus gallus	ENSGALG00000001843	1 retrocopy	retro_ggal_24 ,