RetrogeneDB ID: retro_ggal_23

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: Z:30303187..30304176(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANKRD13C
• Ensembl ID: ENSGALG00000011311
• Aliases: None
• Description: ankyrin repeat domain 13C [Source:HGNC Symbol;Acc:25374]

Sequence

>retro_ggal_23
TTCAAGGGGGACGTGAGGCGGCTGTCAGTGCTCATCCGCACACAGGGCATTGGCCAGAAGGACAGCCATGGAAACACTTC
TTTGCATCTTGCTGTGATGTTGGGACATAAAGAATGTGCCCACTTGCTTTTAGCCCACAATGCTGCAGTAAAGGTGAAAA
ATGCTCAGGGATGGACCACTCTTGCAGAAGCCATCAACTATGGAGACAGAAAAATGATTACAGCAATCCTAAGGAAGCTT
AAACAGCAGTCCAGGGAATCACTGAAGAAAAGCAACCTCGATTATTAAAAGCCCTGAAAGAGCTAGGTGACTTCTCTCTA
GAGCTTCACTGGGATTTTCAAAGTTGGGTGCCTTTACTTTCCTGAATTCTGCCTTCTGATGCATGTAAAATACACAAACA
AGGTATAAATATCAGTCTGGACACAACTCTCATAGATTTTACTGACATGAAGTGCCAATGAGGGGATTTAAGCTTCGTTT
TTAATGGTGATGCAGCACCCTCTGAATCTTTTGTAGTTTTAGACAATGAACAAAAAGTTTACCAGCGAATACATCACGAG
GAATCTGAGATGGAAACAGAGGAAGAGGTTGACATTTTGATGAGCAGTGATATTTACTCAGCAACATTATCAACCAAATC
AGTCACCTTCACACGTGCCCAAATGGGATGGCTTTTTCGAGAAGACAGAACAGAAAGAGTAGGAAACTTTTTGGCAAATT
TCTACCTGGCTAATGGACTTGTATTAGAATCAAGAAAAAGAAGAGAACATCTCAGTGAGGAGGATATTCTTCAAAATAAA
GCTATCATGGAGAGCCTGAGTAAAGGTGGCAACTTAATGGAACAAAACTTTGAACCTGTCAGATGACAATCCCTTACTCC
ACCATCACCCAATACCATTACATGGGAAGAGTACATATCTGCTGAAAATGGAAAAGCTCCTCATCTGAGTAGAGAACTGG
TCTGCGAAGAAAGCAAAAAAACCTTTAAA

Alignment

ORF - retro_ggal_23 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.45 %
• Parental protein coverage: 78.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FKGDVRRLSALIRTQGIGQKDSHGNTPLHLAVMLGHKECAHLLLAHNAPVKVKNAQGWSPLAEAISYGDR
          FKGDVRRLS.LIRTQGIGQKDSHGNT.LHLAVMLGHKECAHLLLAHNA.VKVKNAQGW..LAEAI.YGDR
Retrocopy FKGDVRRLSVLIRTQGIGQKDSHGNTSLHLAVMLGHKECAHLLLAHNAAVKVKNAQGWTTLAEAINYGDR

Parental  QMITALLRKLKQQSRESV-EEKRPRLLKALKELGDFYLELHWDFQSWVPLLSRILPSDACKIHKQGINIR
          .MITA.LRKLKQQSRES..EEK.PRLLKALKELGDF.LELHWDFQSWVPLLS.ILPSDACKIHKQGINI.
Retrocopy KMITAILRKLKQQSRESL<EEKQPRLLKALKELGDFSLELHWDFQSWVPLLS*ILPSDACKIHKQGINIS

Parental  LDTTLIDFTDMKCQRGDLSFIFNGDAAPSESFVVLDNEQKVYQRIHHEESEMETEEEVDILMSSDIYSAT
          LDTTLIDFTDMKCQ.GDLSF.FNGDAAPSESFVVLDNEQKVYQRIHHEESEMETEEEVDILMSSDIYSAT
Retrocopy LDTTLIDFTDMKCQ*GDLSFVFNGDAAPSESFVVLDNEQKVYQRIHHEESEMETEEEVDILMSSDIYSAT

Parental  LSTKSITFTRAQTGWLFREDKTERVGNFLADFYLVNGLVLESRKRREHLSEEDILRNKAIMESLSKGGNL
          LSTKS.TFTRAQ.GWLFRED.TERVGNFLA.FYL.NGLVLESRKRREHLSEEDIL.NKAIMESLSKGGNL
Retrocopy LSTKSVTFTRAQMGWLFREDRTERVGNFLANFYLANGLVLESRKRREHLSEEDILQNKAIMESLSKGGNL

Parental  MEQNFEPVRRQSLTPPSPNTITWEEYISAENGKAPHLGRELVCKESKKTFK
          MEQNFEPVR.QSLTPPSPNTITWEEYISAENGKAPHL.RELVC.ESKKTFK
Retrocopy MEQNFEPVR*QSLTPPSPNTITWEEYISAENGKAPHLSRELVCEESKKTFK

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	0.00 RPM	37.17 RPM
SRP007412_cerebellum	0.04 RPM	38.03 RPM
SRP007412_heart	0.00 RPM	20.41 RPM
SRP007412_kidney	0.06 RPM	41.76 RPM
SRP007412_liver	0.00 RPM	13.39 RPM
SRP007412_testis	0.12 RPM	174.77 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ggal_23 retrocopy.

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_23 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_23 has 0 orthologous retrocopies within neognath group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Gallus gallus	ENSGALG00000011311	1 retrocopy	retro_ggal_23 ,
Rattus norvegicus	ENSRNOG00000011340	2 retrocopies	retro_rnor_2098, retro_rnor_2173,