RetrogeneDB ID: retro_ggal_21

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: AADN03018934.1:879..1977(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA5
• Ensembl ID: ENSGALG00000001000
• Aliases: HSPA5, GRP78
• Description: 78 kDa glucose-regulated protein [Source:UniProtKB/Swiss-Prot;Acc:Q90593]

Sequence

>retro_ggal_21
CCAAGAAACGTGGCGTTCACGCCTGAGGGGGAGCGCCTGATTGGGGATGCAGCCAAGAACCAGCTGACATCCAACCCTGA
GAACACTGTGTTTGATGCCAAGCGGCTCATAGGCCGCACCTGGAATGACCCCTCTGTACAGCAGGACATCAAGTATCTGC
CCTTCAAGGTTGTTGAAAAGAAGGCCAAGCCACATATTCAGGTCGATGTTGGTGGTGGACAAACAAAAACATTTGCTCCT
GAAGAAATTTCTGCCATGGTCCTGACAAAGATGAAAGAAACTGCAGAGGCTTATCTGGGCAAGAAAGTTACTCATGCTGT
TGTTACTGTGCCAGCCTACTTCAATGATGCTCAGCGTCAGGCCACAAAAGATGCTGGTACCATTGCTGGGTTGAACGTGA
TGCGCATTATTAATGAGCCAACTGCTGCTGCAATTGCATACGGATTGGACAAGAGAGAGGGTGAAAAGAACATCCTTGTA
TTTGACCTGGGTGGTGGAACTTTTGATGTCTCCCTCCTGACAATTGACAACGGAGTCTTTGAAGTTGTGGCTACAAATGG
TGACACACACCTGGGTGGAGAAGACTTTGACCAGCGTGTTATGGAGCACTTCATCAAACTCTACAAGAAGAAAACAGGAA
AAGATGTCAGGAAGGATAACAGAGCTGTACAGAAACTAAGACGGGAAGTAGAGAAAGCGAAGCGGGCCCTGTCATCCCAG
CACCAAGCTAGAATTGAAATAGAATCCTTTTTTGAAGGAGAGGATTTCTCTGAGACGCTTACTCGTGCCAAATTTGAAGA
ACTGAATATGGATCTGTTCCGTTCTACGATGAAGCCTGTTCAGAAAGTTCTGGAAGACTCTGACCTAAAGAAGTCTGATA
TTGATGAGATTGTTCTTGTTGGTGGTTCTACTCGCATCCCCAAAATACAACAACTTGTTAAAGAGTTCTTCAATGGGAAA
GAGCCTTCTCGTGGCATTAATCCAGATGAAGCTGTAGCCTATGGTGCAGCTGTTCAGGCTGGTGTTCTCTCTGGGGACCA
AGACACAGGTGACCTGGTGTTGCTTGATGTGTGTCCTCTGACACTTGGCATTGAGACA

Alignment

ORF - retro_ggal_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.45 %
• Parental protein coverage: 56.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSYVAFTPEGERLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKYLPFKVVEKKAKPHIQVDV
          P..VAFTPEGERLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKYLPFKVVEKKAKPHIQVDV
Retrocopy PRNVAFTPEGERLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKYLPFKVVEKKAKPHIQVDV

Parental  GGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEP
          GGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEP
Retrocopy GGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEP

Parental  TAAAIAYGLDKREGEKNILVFDLGGGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKK
          TAAAIAYGLDKREGEKNILVFDLGGGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKK
Retrocopy TAAAIAYGLDKREGEKNILVFDLGGGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKK

Parental  KTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFFEGEDFSETLTRAKFEELNMDLFRSTMKPV
          KTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFFEGEDFSETLTRAKFEELNMDLFRSTMKPV
Retrocopy KTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFFEGEDFSETLTRAKFEELNMDLFRSTMKPV

Parental  QKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTG
          QKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTG
Retrocopy QKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTG

Parental  DLVLLDVCPLTLGIET
          DLVLLDVCPLTLGIET
Retrocopy DLVLLDVCPLTLGIET

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	13.38 RPM	281.14 RPM
SRP007412_cerebellum	5.70 RPM	284.17 RPM
SRP007412_heart	5.32 RPM	274.21 RPM
SRP007412_kidney	19.33 RPM	728.79 RPM
SRP007412_liver	21.97 RPM	1349.91 RPM
SRP007412_testis	6.39 RPM	373.50 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ggal_21 retrocopy.

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_21 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_21 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006880	1 retrocopy	retro_cjac_2221,
Homo sapiens	ENSG00000044574	1 retrocopy	retro_hsap_3005,
Gallus gallus	ENSGALG00000001000	1 retrocopy	retro_ggal_21 ,
Gallus gallus	ENSGALG00000006512	1 retrocopy	retro_ggal_8,
Gorilla gorilla	ENSGGOG00000026879	1 retrocopy	retro_ggor_2082,
Macropus eugenii	ENSMEUG00000016702	1 retrocopy	retro_meug_522,
Mus musculus	ENSMUSG00000026864	1 retrocopy	retro_mmus_1299,
Nomascus leucogenys	ENSNLEG00000017348	1 retrocopy	retro_nleu_751,
Otolemur garnettii	ENSOGAG00000006786	1 retrocopy	retro_ogar_2901,
Pongo abelii	ENSPPYG00000019609	1 retrocopy	retro_pabe_2491,
Pan troglodytes	ENSPTRG00000000563	1 retrocopy	retro_ptro_2033,
Ictidomys tridecemlineatus	ENSSTOG00000011243	4 retrocopies	retro_itri_1686, retro_itri_1687, retro_itri_1689, retro_itri_1879,