RetrogeneDB ID: retro_amel_1881

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195146.1:70441..71294(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL3L
• Ensembl ID: ENSAMEG00000008489
• Aliases: None
• Description: ribosomal protein L3-like [Source:HGNC Symbol;Acc:10351]

Sequence

>retro_amel_1881
ACCATCTTTGCTGAGCACATCCACGATAAGTGCAAAAGGCACTTCTATAAAAACTGGGGTAAGTCTAAGAAGGCCTTCAA
TCAAATACTGCAAGTGGCAGGATAATGACGGCAAGCAGCAGCTAGAGAAGGACTTCAACAGCATGAGGTATGGCCAAATC
ATCCACGTCACCCATACCTAGATGCCCCTACTTCCTCTATGCCAGAAGAAAGCCCATCTTATGGAGGTCCAGGTGAGTAG
AGGCATAGTGGCTGAGAAGCTGGACTAGGCATCCAAGAGCATGGAACAGCAGGTGTTTGTGAACCAAGTGTTTGGGCAGG
ATGAGATGATACATGTCATTAGTGTCACCAAGGGCAAAGGTTACAAAGAGGTCACCAGCCACTGGCACACCAAGAAGCTA
CCCTGCAAAACCCACCAGGGACTGTGCAAGGTGGGCTGTATTGGGGCATGGCATCCTGCCCAAGTGGCCTTCTCCATGGC
ATGGGCTGGGCAGAAAGGCTACCATCACTGCACTGAGATCAACAAGAAGATCTACAAGATTGGCCAGAGCTACCTCATCA
AGGATGGCAAACTGATCAAGAACAATGCTTCCGCTGATTATGATCTGACAAGAGCATAAACCCTCTGAGTCAGCTTTGTC
CACTATGATGAAGTGACCAATGACTTTGTCATGCATAAAGGCTGTGTGATAACCAAGAAGCAAGTGCTTACTCTCCACAA
GTTGTTGCTGGTGCAGATCAAACGGCAGGCCCTGGAGATTGACCTTAAGTTCATTGATACCACCTCCAAGTTTGGCCATG
ACTGATTCCAGACTGTGGAGGATAAGAAAGAATTCATGGGACCACTTATGAAA

Alignment

ORF - retro_amel_1881 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.96 %
• Parental protein coverage: 71.5 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TIFAEHLSDECRRRFYKDWHKSKKKAFT-KACKRWRDADGKKQLQRDLAAMKKYCKVIRVIVHTQMKLLP
          TIFAEH..D.C.R.FYK.W.KSKK.AF..K.CK.W.D.DGK.QL..D...M..Y...I.V..HT.M.LLP
Retrocopy TIFAEHIHDKCKRHFYKNWGKSKK-AFN>KYCK-WQDNDGKQQLEKDFNSMR-YGQIIHV-THT*MPLLP

Parental  FRQKKAHIMEIQLNGGTVAEKVAWAQARLEKQVPVHSVFSQSEVIDVIAVTKGRGVKGVTSRWHTKKLPR
          ..QKKAH.ME.Q...G.VAEK...A....E.QV.V..VF.Q.E.I.VI.VTKG.G.K.VTS.WHTKKLP.
Retrocopy LCQKKAHLMEVQVSRGIVAEKLD*ASKSMEQQVFVNQVFGQDEMIHVISVTKGKGYKEVTSHWHTKKLPC

Parental  KTHKGLRKVACIGAWHPARVGCSIARAGQKGYHHRTELNKKIYRIGRGLHKEDGKVVKNNASTSYDVTDK
          KTH.GL.KV.CIGAWHPA.V..S.A.AGQKGYHH.TE.NKKIY.IG......DGK..KNNAS..YD.T..
Retrocopy KTHQGLCKVGCIGAWHPAQVAFSMAWAGQKGYHHCTEINKKIYKIGQSYLIKDGKLIKNNASADYDLT-R

Parental  SITPLGGFPHYGEVNNDFVMLKGCIAGTKKRVITLRKSLLVHHSRQALENIELKFIDTTSKFGHGRFQTA
          ..T....F.HY.EV.NDFVM.KGC...TKK.V.TL.K.LLV...RQALE.I.LKFIDTTSKFGH..FQT.
Retrocopy A*TL*VSFVHYDEVTNDFVMHKGCVI-TKKQVLTLHKLLLVQIKRQALE-IDLKFIDTTSKFGHD*FQTV

Parental  QEKRVFMGPQKK
          ..K..FMGP..K
Retrocopy EDKKEFMGPLMK

Legend:

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

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_1881 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1881 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008489	1 retrocopy	retro_amel_1881 ,
Ailuropoda melanoleuca	ENSAMEG00000010853	1 retrocopy	retro_amel_1115,
Nomascus leucogenys	ENSNLEG00000008850	9 retrocopies	retro_nleu_1107, retro_nleu_1130, retro_nleu_1249, retro_nleu_1305, retro_nleu_1673, retro_nleu_1824, retro_nleu_2046, retro_nleu_2060, retro_nleu_3126,
Pongo abelii	ENSPPYG00000006973	1 retrocopy	retro_pabe_2854,
Pan troglodytes	ENSPTRG00000007617	12 retrocopies	retro_ptro_1439, retro_ptro_1473, retro_ptro_1753, retro_ptro_2150, retro_ptro_2339, retro_ptro_2462, retro_ptro_2501, retro_ptro_2646, retro_ptro_2741, retro_ptro_2767, retro_ptro_3163, retro_ptro_916,
Ictidomys tridecemlineatus	ENSSTOG00000012921	2 retrocopies	retro_itri_1344, retro_itri_867,