RetrogeneDB ID: retro_ggor_2324

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:28860534..28861953(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IQCB1
• Ensembl ID: ENSGGOG00000028124
• Aliases: None
• Description: None

Sequence

>retro_ggor_2324
GAAGTTAAAAGCCATTGCTGTGCAGGCTTGGAGCCAGGAGAAGATGCAGAGGAACTTTCCAATGAATTACTTCCATCAGC
TGCAGAAAATTTTCTAGTTTTGGGGAGACAATGGCAAACATGTTTTATCAATGCAGCTAAGGCTGAAGAAAAAGATGAGT
TACTAAAAATTGTGACTGATTGGCTCTTCTGGCTTTTGGGAGGCCATGTTGAACTTATTCAGAATGTACTACAAAGTGAT
CGTTTCTTACACTTACTGCAAGTTGACAATGTCCAAATAGGATCGGCACTCATGATGATGCTACAGAATATACTATAGAG
CAACAGTGGTGATTTACTCAGAACAGGAGGAAAAGCCCTGCATTCAATTTTAGATGAAGTTATTTTCAAGCTTTTTTCAA
CTCCTAGTCCAGTCATAAGAAGTACTGCTGCAAAACTCCTACTGTTGATGGCTGAATCCTATCAGGAAATTTTGATTTTA
CTGATACAAAGTGCCTGCTACAAAGGACTCAGAAGTCTACTAAGTAAACAGGAAACTGGGACAGAATTCAGTCAAGAACT
TAGACAGCTCATTGGCCTTTTAAGCCCAGCGGTCTATCAGGAAGTAGAAAAGCAGAAACTACATCAAGCAGCATGCTTGA
TTCAAGCCTATTGGAAGGGTTTTCAGACAAGAAAGAGATTAAAGAAGCTTCCATCTGCTGTGATTGCTTTGCAGAGGAGT
TTCAGACCTAAACGAACAAAGATGTTGCTGGAGATAAATAGGAAGAAGGAAGAAGAGGACCTCAGATTGCGATTGCAACT
TCAAAGACAGAGAGCCATGAGACTTTCCCAAGAATTGCGGCTGAGTATGCTCAAAGTAGTTCATCCAGGTCAAGTGGAGA
AACACAATTGGGAAATGGAAGAGAAATCAGCACTGATTATCCAGAAACATTGGAGAGGGTACAGGGAAAGGAAAAATTTT
TGCCAACAGAGGCAGTCTCTCACAGAATATAAAGCAGCTGTCATACTTCAAAGAGCAGTGTTTAAATTCCTAGCAAAGTG
CCGTAAGAAACAGAAACTATTTGTTCCTTGGCGAGGACTCCAAGAACTCACTGATGCATGCCGAGCTGAACTGAAGCAAC
AAGCGGATGACTATGTCAGAAGACATTCGGGCTCTCCAATGTCAGATGTGGTCAGTAGGGAGCTCCATGCCCAAGCTTAA
GAACGACTGCAACACTACTTTATGGGCAGGGCCCTGGAAGAGTGAGCCCAGCAACACAGAGAAGCTCTGATGGTACAGAT
CAGCACTAACGTTGAACAGCTAATGAAGGCACCAAGTCTGAAGGAAGCAGAAGGGAAAGAACCTGAGCTCTTCCTAAGAT
CCAGGCCTGTGGCAGCCAAGGCCAAGCAGGCCCATCTCACCACCCTGAAGCATATACAA

Alignment

ORF - retro_ggor_2324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.01 %
• Parental protein coverage: 79.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QILSHCCVGLEPGEDAEEFYNELLPSAAEHFLVLGRQLQTCFINAAKAEEKDELLHFFQIVTDSLFWLLG
          ...SHCC.GLEPGEDAEE..NELLPSAAE.FLVLGRQ.QTCFINAAKAEEKDELL....IVTD.LFWLLG
Retrocopy EVKSHCCAGLEPGEDAEELSNELLPSAAENFLVLGRQWQTCFINAAKAEEKDELL---KIVTDWLFWLLG

Parental  GHVELIQNVLQSDHFLHLLQADNVQIGSAVMMMLQNILQINSGDLLRIGRKALYSILDEVIFKLFSTPSP
          GHVELIQNVLQSD.FLHLLQ.DNVQIGSA.MMMLQNIL..NSGDLLR.G.KAL.SILDEVIFKLFSTPSP
Retrocopy GHVELIQNVLQSDRFLHLLQVDNVQIGSALMMMLQNIL*SNSGDLLRTGGKALHSILDEVIFKLFSTPSP

Parental  VIRSTATKLLLLMAESHQEILILLRQSTCYKGLRRLLSKQETGTEFSQELRQLVGLLSPTVYQEVEEQKL
          VIRSTA.KLLLLMAES.QEILILL.QS.CYKGLR.LLSKQETGTEFSQELRQL.GLLSP.VYQEVE.QKL
Retrocopy VIRSTAAKLLLLMAESYQEILILLIQSACYKGLRSLLSKQETGTEFSQELRQLIGLLSPAVYQEVEKQKL

Parental  HQAACLIQAYWKGFQTRKRLKKLPSAVIALQRSFRTKKKIPLLSLCNQKRLLDIIIYSQLEVRNRGSFLS
          HQAACLIQAYWKGFQTRKRLKKLPSAVIALQRSFR.K....LL.....K...D.....QL..R.R...LS
Retrocopy HQAACLIQAYWKGFQTRKRLKKLPSAVIALQRSFRPKRTKMLLEINRKKEEEDLRLRLQLQ-RQRAMRLS

Parental  LFEYVVIVSIIFLGQVEKHYREMEEKSALIIQKHWRGYRERKNFHQQRQSLIEYKAAVTLQRKALKFLVK
          .............GQVEKH..EMEEKSALIIQKHWRGYRERKNF.QQRQSL.EYKAAV.LQR...KFL.K
Retrocopy QELRLSMLKVVHPGQVEKHNWEMEEKSALIIQKHWRGYRERKNFCQQRQSLTEYKAAVILQRAVFKFLAK

Parental  CRKKKKLFAPWRGLQELTDARRVELKKQVDDYVRRHLGSPMSDVVSRELHAQAQERLQHYFMGRALEERA
          CRKK.KLF.PWRGLQELTDA.R.ELK.Q.DDYVRRH.GSPMSDVVSRELHAQA.ERLQHYFMGRALEE.A
Retrocopy CRKKQKLFVPWRGLQELTDACRAELKQQADDYVRRHSGSPMSDVVSRELHAQA*ERLQHYFMGRALEE*A

Parental  QQHREALMAQISTNVEQLMKAPSLKEAEGKEPELFLSRSRPVAAKAKQAHLTTLKHIQ
          QQHREALM.QISTNVEQLMKAPSLKEAEGKEPELFL.RSRPVAAKAKQAHLTTLKHIQ
Retrocopy QQHREALMVQISTNVEQLMKAPSLKEAEGKEPELFL-RSRPVAAKAKQAHLTTLKHIQ

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_prefrontal_cortex	0.29 RPM	4.32 RPM
SRP007412_cerebellum	0.39 RPM	5.63 RPM
SRP007412_heart	0.00 RPM	0.91 RPM
SRP007412_kidney	0.25 RPM	2.62 RPM
SRP007412_liver	0.26 RPM	3.30 RPM
SRP007412_testis	3.11 RPM	30.04 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2324 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2324 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3441
Pan troglodytes	retro_ptro_2333
Pongo abelii	retro_pabe_2845

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000173226	1 retrocopy	retro_hsap_3441,
Gorilla gorilla	ENSGGOG00000028124	1 retrocopy	retro_ggor_2324 ,
Otolemur garnettii	ENSOGAG00000004271	1 retrocopy	retro_ogar_3056,
Pongo abelii	ENSPPYG00000013494	1 retrocopy	retro_pabe_2845,
Pan troglodytes	ENSPTRG00000015281	1 retrocopy	retro_ptro_2333,